| 1 | implicit integer*4 (i-n)
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| 2 | implicit real*8 (a-h,o-z)
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| 3 | character*255 version
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| 4 |
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| 5 | integer MAX_REPLICA, MAX_PROC
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| 6 |
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| 7 | PARAMETER(MAX_PROC=2048)
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| 8 | parameter (MAX_REPLICA = 2048) ! max. number of replicas
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| 9 | parameter (mxml=10) ! max. number of molecules
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| 10 | parameter(mxrs=100) ! max. total number of residues
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| 11 | parameter(mxat=2600) ! max. total number of atoms
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| 12 | parameter(mxbd=3) ! max. number of bonds to following atoms
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| 13 | parameter(mxath=100) ! max. number of atoms in help-arrays
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| 14 | parameter(mxvr=mxrs*8) ! max. number of local variables
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| 15 | parameter(mxms=mxvr*3) ! max. total number of moving sets
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| 16 | parameter(mxvw=mxat*4) ! max. number of vwd domains
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| 17 | parameter(mx14=mxat*4) ! max. number of '1-4' partners
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| 18 | parameter(mxvrh=mxath) ! max. number of variables in help
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| 19 | parameter(mxtyat=18) ! max. # of energetic atom-types
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| 20 | parameter(mxhbdo=4) ! max. types of Hydrogens as donors in HB
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| 21 |
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| 22 | parameter (mxhbac=6) ! max. types of atoms as acceptors in HB
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| 23 | parameter(mxtybl=0) ! max. # of types of bond length potentials
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| 24 | parameter(mxtyba=0) ! - " - b. angle pot.
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| 25 | parameter(mxtyto=19) ! - " - torsional pot.
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| 26 | parameter(mxrt=500) ! max. # of restraint types
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| 27 | parameter(mxvrrt=mxrt*2) ! max. # of restraint variables
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| 28 | parameter(mxrtsu=mxvr*6) ! max. # of pointers subsets -> restraints
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| 29 | parameter(nrsty=35) ! max. # of residue types
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| 30 |
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| 31 | parameter (pi=3.141592653589793d0)
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| 32 | parameter(pi2=2.d0*pi)
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| 33 | parameter(pi4=4.d0*pi)
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| 34 | parameter(crd=57.2957795130823d0)
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| 35 | parameter(cdr=1.745329251994330d-2)
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| 36 |
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| 37 | parameter (izero=0)
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| 38 | parameter(ione=1)
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| 39 | parameter(zero=0.d0)
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| 40 | parameter(one=1.d0)
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| 41 | parameter (version= &
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| 42 | & '$Id: INCL.H 335 2007-08-09 09:32:21Z meinke $')
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| 43 |
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| 44 | integer seed
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| 45 | integer enysolct
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| 46 | common /counter/enysolct
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| 47 | common /commonrandom/ seed
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| 48 | common /bounds/ boxsize
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| 49 |
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| 50 | integer myrank, no, my_mpi_comm
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| 51 | integer workPerProcessor(0:mxml, 0:MAX_PROC)
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| 52 | common/paral/myrank,no,my_mpi_comm,workPerProcessor
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| 53 | common /bet/beta
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| 54 | !== For solvent============================
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| 55 | parameter (mxpoint=2000) !
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| 56 | parameter(mxbox=80000) !
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| 57 | parameter(mxinbox=80000) !
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| 58 | parameter(mxtysol=9) !Max number of solvent types
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| 59 | parameter (rwater=1.4) !The Wdv radius of the water molecule
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| 60 |
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| 61 | !== Solvent types
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| 62 | logical isolscl
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| 63 | common /isolty/ itysol, isolscl
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| 64 | common /tes/ spoint(mxpoint,3)
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| 65 | common /pnt/ npnt
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| 66 | common /sol/ coef_sl(mxtysol,mxtyat),rad_vdw(mxtysol,mxtyat)
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| 67 | common/ressurf/surfres(mxrs)
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| 68 | dimension rsstrg(mxrs)
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| 69 | common /abgncor/rsstrg
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| 70 |
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| 71 | !---- The vdW radii of the atoms and solvation coefficients
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| 72 | common /solvent/ rvdw(mxat),sigma(mxat)
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| 73 |
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| 74 | ! vdvol - van der Waals volume of the molecule
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| 75 | ! asa - Surface of molecule
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| 76 | common /v_sol/ vdvol,asa,asap,asah
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| 77 |
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| 78 | ! gradan - analytical gradients of solv. energy against atomic coordinates
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| 79 | common /deriv/ gradan(mxat,3)
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| 80 |
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| 81 |
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| 82 | !-----For calculation of hydrogen bonds
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| 83 | parameter(mxtyhb=100) ! Maximum number of hydrogen bond types
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| 84 | common /h_bond/ ntyhb,ixtyhb(mxtyhb),nutyhb(mxtyhb), &
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| 85 | & mmhb(mxml, mxml)
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| 86 | !-----For molecule parameter
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| 87 | common/mol_par/ nvr
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| 88 |
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| 89 | !-----Hydrophobic/polar radius of gyration
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| 90 | common /rgy/ rgyh, rgyp
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| 91 | !=======================================
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| 92 |
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| 93 | character nmrt(mxrt)*4,nmvrrt(mxvrrt)*3
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| 94 | character rsnmcd(nrsty)*4,onltcd(nrsty)
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| 95 | character nmath(mxath)*4,nmvrh(mxvrh)*3
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| 96 | logical flex, tesgrd,epsd,sh2
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| 97 | ! -----Switches for Bias Gaussian Steps and random order in variable updates
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| 98 | ! upchswitch=0 => No BGS
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| 99 | ! upchswitch=1 => For backbone updates, use BGS with probability bgsprob
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| 100 | ! upchswitch=2 => More sophisticated, temperature dependent choice between
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| 101 | ! simple pivot update and BGS
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| 102 | logical rndord
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| 103 | integer upchswitch
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| 104 | double precision bgsprob
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| 105 | common /updchois/rndord,upchswitch,bgsprob
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| 106 | common /con_i/ idloa,idloz,idupa,idupz
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| 107 | !---- The contact matrix and the indices of C_alpha atoms
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| 108 | common/cont_i_j/ ijcont(mxrs,mxrs),ind_alf(mxrs)
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| 109 | common /jref/ iref(mxrs,mxrs),nci
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| 110 |
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| 111 | !-----For calculation of Zimmermann code of conformation:
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| 112 | character zimm*(mxrs)
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| 113 | common/zimme/zimm
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| 114 |
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| 115 | ! lunlib - LUN of residue library
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| 116 | ! lunseq - LUN of sequence file
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| 117 | ! lunchg - LUN of charges for terminal residues (=0 if not necessary)
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| 118 | ! lunvar - LUN of file with commands to set variables
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| 119 | ! lunrst - LUN for variable restraints
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| 120 | ! reslib - name of residue library
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| 121 | ! seqfil - name of sequence file
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| 122 | ! chgfil - name of file with charges for terminal residues
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| 123 | ! varfil - name of file with commands to set variables
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| 124 | ! rstfil - name of file with variable restraints
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| 125 |
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| 126 | common /fil_i/ lunlib,lunseq,lunchg,lunvar,lunrst
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| 127 | character reslib*80,seqfil*80,chgfil*80,varfil*80,rstfil*80
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| 128 | common /fil_c/ reslib,seqfil,chgfil,varfil,rstfil
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| 129 |
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| 130 | ! ntlml - total number of molecules
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| 131 | ! irsml1,irsml2 - indices of 1st/last residue of each molecule
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| 132 | ! ivrml1,nvrml - index of 1st/number of loc. variables in molecule
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| 133 | ! imsml1,nmsml - index of 1st/number of moving sets in molecule
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| 134 | ! iadml1,nadml - index of 1st/number of 'added varaibles' in molecule
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| 135 | ! nmml - name of molecule
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| 136 |
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| 137 | ! -------------------------------------------------------------- new
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| 138 | ! ixrfpt - indices of 3 reference points (first 3 backbone atoms)
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| 139 | ! per molecule
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| 140 | ! ixatp - pointer of each SMMP atom to corresponding atom in a ref.
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| 141 | ! structure, (=0 if no corr. atom in ref. str.)
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| 142 | ! isrfvr() = true, if i-th variable is defined in ref. structure
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| 143 | ! rfpt - coordinates of a reference point (first bb atom) in molecule
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| 144 | ! xrfax,yrfax,zrfax - direction cosines of 3 ref. axes (axes J,K,L
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| 145 | ! according to global angles alpha,beta,gamma)
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| 146 | ! gbpr - 6 global parameters per molecule (3 shifts, 3 angles)
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| 147 | ! --------------------------------------------------------------------
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| 148 |
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| 149 | common /mol_i/ ntlml,irsml1(mxml),irsml2(mxml),ivrml1(mxml), &
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| 150 | &nvrml(mxml),imsml1(mxml),nmsml(mxml),iadml1(mxml),nadml(mxml) &
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| 151 | &,ixrfpt(3,mxml) &
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| 152 | &,ixatp(mxat) &
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| 153 | &,ireg
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| 154 | ! -------------------
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| 155 |
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| 156 | logical isrfvr(mxvr)
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| 157 | common /refstr/ isrfvr
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| 158 |
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| 159 | character nmml(mxml)*80
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| 160 | common /mol_c/ nmml
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| 161 |
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| 162 | ! ----------------------------------------- new
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| 163 | common /mol_r/ rfpt(3,mxml),gbpr(6,mxml), &
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| 164 | &xrfax(3,mxml),yrfax(3,mxml),zrfax(3,mxml)
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| 165 | ! ---------------------------------------------
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| 166 |
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| 167 | ! iatrs1,iatrs2 - indices of 1st (backbone)/last atom of residue
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| 168 | ! ixatrs - index of last backbone atom (may be bound to next res.)
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| 169 | ! ivrrs1,nvrrs - index of 1st/number of local variable for residue
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| 170 | ! seq - names of residues
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| 171 |
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| 172 | common /res_i/ iatrs1(mxrs),iatrs2(mxrs),ixatrs(mxrs),ivrrs1(mxrs)&
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| 173 | & ,nvrrs(mxrs)
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| 174 | character seq(mxrs)*4
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| 175 | common /res_c/ seq
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| 176 |
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| 177 | ! ityat - atom class
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| 178 | ! iowat - index of preceeding atom (=0 if none)
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| 179 | ! iyowat - type of bond with prec. atom (=1:single bond,=-1:not single)
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| 180 | ! nbdat - number of bonds with following atoms
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| 181 | ! ibdat - indices of following covalently bonded atoms
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| 182 | ! iybdat - types of covalently bonds to following atoms (see 'iyowat')
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| 183 | ! ixmsat - index of the moving set for each atom
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| 184 | ! cgat - point charge at atom
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| 185 | ! xbaat - |
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| 186 | ! ybaat - | axis to alter valence-angle for i-th atom
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| 187 | ! zbaat - | (placed at 'iowat(i)')
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| 188 | ! baat - valence angle 'iowat(iowat(i)), iowat(i), i' [rad.]
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| 189 | ! snbaat - Sin(baat)
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| 190 | ! csbaat - Cos(baat)
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| 191 | ! xtoat - |
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| 192 | ! ytoat - | axis between 'iowat(i)' and i-th atom
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| 193 | ! ztoat - |
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| 194 | ! toat - dihedral 'iowat(iowat(iowat(i))), iowat(iowat(i)),
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| 195 | ! iowat(i), i' [rad.]
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| 196 | ! sntoat - Sin(toat)
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| 197 | ! cstoat - Cos(toat)
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| 198 | ! blat - valence-length 'iowat(i)-i'
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| 199 | ! xat - |
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| 200 | ! yat - | cartesian coordinates of atom
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| 201 | ! zat - |
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| 202 | ! nmat - atom name
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| 203 |
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| 204 | common /atm_i/ ityat(mxat),iowat(mxat),iyowat(mxat),nbdat(mxat), &
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| 205 | & ibdat(mxbd,mxat),iybdat(mxbd,mxat),ixmsat(mxat)
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| 206 | common /atm_r/ cgat(mxat), &
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| 207 | &xbaat(mxat),ybaat(mxat),zbaat(mxat),baat(mxat),snbaat(mxat), &
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| 208 | &csbaat(mxat), &
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| 209 | &xtoat(mxat),ytoat(mxat),ztoat(mxat),toat(mxat),sntoat(mxat), &
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| 210 | &cstoat(mxat), &
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| 211 | &blat(mxat), &
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| 212 | &xat(-1:mxat),yat(-1:mxat),zat(-1:mxat)
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| 213 | character nmat(mxat)*4
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| 214 | common /atm_c/ nmat
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| 215 |
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| 216 | ! olvlvr - stores initial values for internal variables
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| 217 | ! nmvr - name of variable
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| 218 | ! iatvr - index of primary moving atom for loc. variable
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| 219 | ! ityvr - type of variable ( 1 = valence length,
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| 220 | ! 2 = valence angle,
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| 221 | ! 3 = dihedral angle)
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| 222 | ! iclvr - indicates class for corresponding variable potential
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| 223 | ! iorvr - indicates appropriate order of variables
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| 224 | ! imsvr - index of 1st moving set per variable as stored in
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| 225 | ! 'latms1,latms2'
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| 226 | ! imsvr1,imsvr2 - indices of 1st & last moving set per variable
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| 227 | ! 'latms1,latms2'
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| 228 | ! latms1,latms2 - lists of indices for 1st and last atom of each moving set
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| 229 | ! iadvr1,iadvr2 - indices of 1st & last related variable per var. in 'ladvr'
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| 230 | ! ladvr - list of variable indices which are related to other variables
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| 231 | ! fxvr - .true. if variable will be fixed throughout calculations
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| 232 |
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| 233 | common /var_r/ olvlvr(mxvr),vlvr(mxvr),axvr(mxvr)
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| 234 | common /var_i/ iatvr(mxvr),ityvr(mxvr),iclvr(mxvr),iorvr(mxvr), &
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| 235 | & imsvr1(mxvr),imsvr2(mxvr),latms1(mxms),latms2(mxms)&
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| 236 | & ,iadvr1(mxvr),iadvr2(mxvr),ladvr(mxvr),idvr(mxvr)
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| 237 | character nmvr(mxvr)*3
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| 238 | common /var_c/ nmvr
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| 239 | logical fxvr(mxvr)
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| 240 | common /var_l/ fxvr
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| 241 |
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| 242 | ! Energy parametrization for SCHERAGA set
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| 243 | !
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| 244 | ! ehm - 1.5*(elem. charge)/(Planck\'s const./2Pi * electr. mass)
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| 245 | ! atpl - atomic polarizabilities
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| 246 | ! efel - empirical numbers of effective electrons per atom
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| 247 | ! emin - minima of pairwise Lennard-Jones terms of like atoms
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| 248 | ! rmin - corresponding pair-distance of energy minima
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| 249 | ! chb_s,ahb_s - parameter of attraction/repulsion terms of HB-potential
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| 250 | ! e0to_s,sgto_s,rnto_s - barrier[kcal/mole],sign,multiplicity of tors.potential
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| 251 | ! eps_s - distance-INdependent diel. constant
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| 252 | ! do_s,ac_s - flag to define atom-types serving as donors/acceptors in HB
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| 253 |
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| 254 | common /sche_r/ ehm,atpl(mxtyat),efel(mxtyat),emin(mxtyat), &
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| 255 | & rmin(mxtyat),chb_s(mxhbdo,mxhbac),ahb_s(mxhbdo,mxhbac), &
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| 256 | & e0to_s(mxtyto),sgto_s(mxtyto),rnto_s(mxtyto), &
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| 257 | & eps_s
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| 258 | logical do_s(mxtyat),ac_s(mxtyat)
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| 259 | common /sche_l/ do_s,ac_s
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| 260 |
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| 261 | ! Energy parametrization for FLEX set
|
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| 262 | !
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| 263 | ! c_f,a_f - parameter of attraction/repulsion terms of LJ-potential
|
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| 264 | ! chb_f,ahb_f - parameter of attraction/repulsion terms of HB-potential
|
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| 265 | ! e0to_s,sgto_s,rnto_s - barrier[kcal/mole],sign,multiplicity of tors.potential
|
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| 266 | ! plt_f,slp_f - parameters for sigmoidal distance-dependent epsilon
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| 267 | ! cohb_f - cut-off distance between H- & acceptor atom in Hydrogen-Bonds
|
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| 268 | ! do_f,ac_f - flags atom-types serving as donors/acceptors in HB
|
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| 269 |
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| 270 | common /flex_r/ c_f(mxtyat,mxtyat),a_f(mxtyat,mxtyat), &
|
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| 271 | & chb_f(mxhbdo,mxhbac),ahb_f(mxhbdo,mxhbac), &
|
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| 272 | & e0to_f(mxtyto),sgto_f(mxtyto),rnto_f(mxtyto), &
|
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| 273 | & plt_f,slp_f,cohb_f
|
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| 274 | logical do_f(mxtyat),ac_f(mxtyat)
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| 275 | common /flex_l/ do_f,ac_f
|
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| 276 |
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| 277 | ! Currently chosen energy parametrization
|
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| 278 | !
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| 279 | ! ihbty = 1, i - HB donor hydrogen & j - HB acceptor
|
|---|
| 280 | ! = -1, i - HB acceptor & j - HB donor hydrogen
|
|---|
| 281 | ! = 0, otherwise
|
|---|
| 282 | ! cij,aij - parameters of attraction/repulsion terms of LJ-potential
|
|---|
| 283 | ! a14 - special value for repulsion in "1-4"-interactions
|
|---|
| 284 | ! chb,ahb - parameters of attraction/repulsion terms of HB-potential
|
|---|
| 285 | ! e0to,sgto,rnto - barrier*0.5 !!,sign,multiplicity of torsional potential
|
|---|
| 286 | ! esnto = e0/2 * sign * multipl.
|
|---|
| 287 | ! conv - parameter to convert electrostat. energy into [kcal/mole]
|
|---|
| 288 | ! plt,slp,cohb - see FLEX
|
|---|
| 289 | ! flex - .true. if FLEX-parametrization is to be used (obsolete)
|
|---|
| 290 | ! ientyp : 0 => ECEPP, 1 => FLEX, 2 => Lund, 3 => ECEPP+Abagyan
|
|---|
| 291 | ! tesgrd - .true. if GRADTEST to be included
|
|---|
| 292 |
|
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| 293 | common /epar_i/ ihbty(mxtyat,mxtyat)
|
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| 294 | common /epar_r/ cij(mxtyat,mxtyat),aij(mxtyat,mxtyat), &
|
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| 295 | & a14(mxtyat,mxtyat),chb(mxtyat,mxtyat),ahb(mxtyat,mxtyat), &
|
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| 296 | & e0to(mxtyto),sgto(mxtyto),rnto(mxtyto),esnto(mxtyto), &
|
|---|
| 297 | & conv, plt,slp, cohb
|
|---|
| 298 |
|
|---|
| 299 | common /epar_l/ flex, tesgrd,sh2,epsd,ientyp
|
|---|
| 300 |
|
|---|
| 301 | ! ENERGY & -MINIMIZATION
|
|---|
| 302 |
|
|---|
| 303 | ! nvwml,ivwml1 - number/index of 1st vdW-domain per molecule
|
|---|
| 304 | ! ivwat1,ivwat2 - index of 1st/last vdW-domain per atom
|
|---|
| 305 | ! lvwat1,lvwat2 - lists of indices of 1st and last atom in each vdw domain
|
|---|
| 306 | ! n14ml,i14ml1 - number/index of 1st '1-4' interaction partner per molecule
|
|---|
| 307 | ! i14at1,i14at2 - index of 1st/last '1-4' interact. partner per atom
|
|---|
| 308 | ! ixatvw - index of respective atom for each vdW-domain
|
|---|
| 309 | ! ixatvw - index of respective atom for each '14'-interaction partner
|
|---|
| 310 |
|
|---|
| 311 | ! ---------------------------------------------------------------------------- new
|
|---|
| 312 | ! eyel,eyvw,eyhb,eyvr,eysm,eysl,eyrg - Coulomb,vdW,HB,variable-potential & total
|
|---|
| 313 | ! eyslh, eyslp - hydrophilic (h)/phobic (p) conributions to the solvent energy
|
|---|
| 314 | ! potential energy, solvation, regularization energy
|
|---|
| 315 | ! gdeyvr - partial derivative of total energy vs. variable (Gradient)
|
|---|
| 316 | ! gdeyrg - partial derivative of regularization energy vs. variable (Gradient)
|
|---|
| 317 | ! gdeysl - partial derivative of solvatation energy vs. variable (Gradient)
|
|---|
| 318 | ! wtey - weight to energy & energy gradient
|
|---|
| 319 | ! wtrg - weight to reg. target & its gradient
|
|---|
| 320 | common /eny_i/ nvwml(mxml),ivwml1(mxml),n14ml(mxml),i14ml1(mxml), &
|
|---|
| 321 | & ivwat1(mxat),ivwat2(mxat),i14at1(mxat),i14at2(mxat)&
|
|---|
| 322 | & ,lvwat1(mxvw),lvwat2(mxvw),l14at(mx14) &
|
|---|
| 323 | & ,ixatvw(mxvw),ixat14(mx14)
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| 324 | common /eny_r/ eyel,eyvw,eyhb,eyvr,eysm,eysl,eyrg,eyslh,eyslp,eyab&
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| 325 | & ,eysmi,eyhbi,eyeli,eyvwi &
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| 326 | & ,gdeyvr(mxvr),gdeyrg(mxvr),gdeysl(mxvr) &
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| 327 | & ,gdeygb(6*mxml),wtey,wtrg
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| 328 |
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| 329 | ! ntlrt - total # of restraint types
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| 330 | ! ntlsu - total # of variable subsets
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| 331 | ! nmrt - name of r.t
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| 332 | ! pbrt - probability for r.t
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| 333 | ! i1vrrt,i2vrrt - 1st,last restraint variable for a r.t
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| 334 | ! nmvrrt - name of restraint variable
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| 335 | ! vuvrrt - average value for r.v
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| 336 | ! dvvrrt - standard deviation for r.v
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| 337 | ! i1rtsu - point to 1st restraint type for a variable subset
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| 338 | ! nprtsu - # of restraint types for each subset
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| 339 | ! iprtsu - pointers from subsets --> restr. types
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| 340 | ! i1vrsu,i2vrsu - 1st,last pointer in 'ipvrsu' per var. subset
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| 341 | ! ipvrsu - pointers var. subset -> variables
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| 342 |
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| 343 | common /rstr_i/ ntlrt,ntlsu,i1vrrt(mxrt),i2vrrt(mxrt), &
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| 344 | & iprtsu(mxrtsu),i1rtsu(mxvr),nrtsu(mxvr), &
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| 345 | & i1vrsu(mxvr),i2vrsu(mxvr),ipvrsu(mxvr)
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| 346 |
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| 347 | common /rstr_c/ nmrt,nmvrrt
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| 348 | common /rstr_r/ pbrt(mxrt),vuvrrt(mxvrrt),dvvrrt(mxvrrt)
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| 349 |
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| 350 | ! rsnmcd - 4-letter codes for NRSTY residue types
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| 351 | ! onltcd - respective 1-letter codes for residue types
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| 352 |
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| 353 | common /rsnm_c/ rsnmcd,onltcd
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| 354 |
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| 355 | ! arrays for help
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| 356 |
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| 357 | common /help_i/ ityath(mxath),iowath(mxath),iyowath(mxath), &
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| 358 | & nbdath(mxath),ibdath(mxbd,mxath), &
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| 359 | & iybdath(mxbd,mxath), &
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| 360 | & ityvrh(mxvrh),iclvrh(mxvrh),iatvrh(mxvrh)
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| 361 | common /help_r/ blath(mxath),baath(mxath),toath(mxath), &
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| 362 | & cgath(mxath)
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| 363 | common /help_c/ nmath,nmvrh
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| 364 |
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