source: init_energy.f

Last change on this file was 38d77eb, checked in by baerbaer <baerbaer@…>, 14 years ago

Redirected standard out to logString.

SMMP produced a lot of log messages. This became an issue when run in massively
parallel environments. I replaced all writes to standard out to a write to logString.
The next step is to pass this string to a function that writes the messages to a log
file according to their importance and the chosen log level.

git-svn-id: ​svn+ssh://svn.berlios.de/svnroot/repos/smmp/trunk@34 26dc1dd8-5c4e-0410-9ffe-d298b4865968
  • Property mode set to 100644
File size: 23.2 KB
RevLine 
[bd2278d]1! **************************************************************
2!
3! This file contains the subroutines: init_energy,setpar
4! This file contains a BLOCK DATA statement
5!
6! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
[32289cd]7! Shura Hayryan, Chin-Ku
[bd2278d]8! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
9! Jan H. Meinke, Sandipan Mohanty
10!
11! **************************************************************
[e40e335]12
13
14 subroutine init_energy(libdir)
15
[bd2278d]16! ----------------------------------------------
17! PURPOSE: initialize energy parameters
18! 0 => ECEPP2 or ECEPP3 depending on the value of sh2
[32289cd]19! 1 => FLEX
[bd2278d]20! 2 => Lund force field
21! 3 => ECEPP with Abagyan corrections
22!
23!
24! CALLS: setpar, tessel,iendst
25!
26! contains: BLOCK DATA
27! ----------------------------------------------
[e40e335]28
29 include 'INCL.H'
30
[32289cd]31 integer ll, iendst, its
32
[e40e335]33 character libdir*(*),tesfil*80
[32289cd]34
[e40e335]35 if (ientyp.eq.1) then
36 flex = .true.
[32289cd]37 else
[e40e335]38 flex = .false.
39 end if
[32289cd]40
[e40e335]41 lunlib=10
42 ll=iendst(libdir)
43
44 if (flex) then ! Flex
45
46 reslib=libdir(1:ll)//'lib.flx'
47 lunchg=12
48 chgfil=libdir(1:ll)//'charges'
49
50 else
51
52 if (sh2) then ! Scheraga (ECEPP/2)
53 reslib=libdir(1:ll)//'lib.sh2'
54 else ! Scheraga (ECEPP/3)
55 reslib=libdir(1:ll)//'lib.sh3'
56 endif
57
58 endif
59
[32289cd]60 if (ientyp .eq. 2) then
[c076b43]61 reslib=libdir(1:ll)//'lib.lun'
62 endif
63
[e40e335]64 call setpar() ! Initialize force field parameters
65
66
[bd2278d]67!----Initialize solvation part if necessary
[38d77eb]68 write (logString, *) 'init_energy: itysol = ',itysol
69 write (logString, *) 'init_energy: esol_scaling = ',isolscl
[e40e335]70
71 its = iabs(itysol)
72
73 if (its.gt.0.and.its.le.mxtysol) then
74
75 ll=iendst(libdir)
76 tesfil = libdir(1:ll)//'tes.dat'
77 open(unit=20,file=tesfil,status='old',err=10)
78 call tessel()
79 close(20)
80
81 else
[32289cd]82
[e40e335]83 if (itysol.ne.0) then
[38d77eb]84 write (logString, '(a)')
85 & ' init_energy> undefined solvent type !'
[e40e335]86 stop
87 endif
88
89 endif
90
[bd2278d]91! ___________________________ initialise COMMON 'con_r'
[e40e335]92 idloa=ichar('a')
93 idloz=ichar('z')
94 idupa=ichar('A')
95 idupz=ichar('Z')
96
97 return
98
[38d77eb]99 10 write (logString, '(a)')
100 & 'Cannot open the file with surface points'
[e40e335]101 stop
102
103 end
104
[bd2278d]105! *********************
[e40e335]106 subroutine setpar
107
[bd2278d]108! __________________________________________________________
109! PURPOSE: initialize parameter set for empirical potentials
110! depending on variable 'flex'
111!
112! CALLS: None
113! __________________________________________________________
[e40e335]114
115 include 'INCL.H'
116
[32289cd]117 double precision hbc, hba, ri, ai, aei, aic, a, aj, c, rij
118
119 integer i, j, iac, ido, jac, jdo
120
[e40e335]121 dimension hbc(mxhbdo,mxhbac),hba(mxhbdo,mxhbac)
122 logical do(mxtyat),ac(mxtyat)
123
124
125 tesgrd = .false. ! numerical check of analytical gradients
126
[bd2278d]127! ______________________________________ Lennard-Jones parameters
[e40e335]128 if (flex) then
129
130 plt=plt_f
131 slp=slp_f
132 cohb=cohb_f
133
134 do i=1,mxtyat
135 do j=1,i
136 cij(i,j)=c_f(i,j)
137 cij(j,i)=cij(i,j)
138 aij(i,j)=a_f(i,j)*1000
139 aij(j,i)=aij(i,j)
140 enddo
141 do j=1,mxtyat
142 a14(i,j)=aij(i,j)
143 enddo
144
145 do(i)=do_f(i)
146 ac(i)=ac_f(i)
147 enddo
148
149 do i=1,mxhbdo
150 do j=1,mxhbac
151 hbc(i,j)=chb_f(i,j)
152 hba(i,j)=ahb_f(i,j)
153 enddo
154 enddo
155
156 do i=1,mxtyto
157 e0to(i)=e0to_f(i)/2.
158 sgto(i)=sgto_f(i)
159 rnto(i)=rnto_f(i)
160 enddo
161
162 else ! ---------------------- Scheraga:
163
164 conv=conv/eps_s
165
166 do i=1,mxtyat
167 atpl(i)=atpl(i)/100
168 efel(i)=efel(i)/100
169 emin(i)=emin(i)/1000
170 rmin(i)=rmin(i)/100
171 enddo
172
173 do i=1,mxtyat
174 ri=rmin(i)
175 ai=atpl(i)
176 aei=sqrt(ai/efel(i))
[bd2278d]177!c aic=ai/ehm !! ICM
178!c do j=i,mxtyat !! -"-
[e40e335]179 aic=ai*ehm !! comment for ICM:
180 cij(i,i)=aic*ai/(aei+aei) !! -"-
181 a=.5*cij(i,i)*ri**6
182 aij(i,i)=a !!
183 a14(i,i)=.5*a !!
184 do j=i+1,mxtyat !!
185 aj=atpl(j)
[bd2278d]186! _______ Constant for 6-12 attractive term (Slater-Kirkwood formula)
[e40e335]187 c=aic*aj/(aei+sqrt(aj/efel(j)))
188 cij(i,j)=c
189 cij(j,i)=c
[bd2278d]190! ____________________________ repulsive term (form. 3 & 6 of ref 2)
[e40e335]191 rij=.5*(ri+rmin(j))
192 a=.5*c*rij**6
193 aij(i,j)=a
194 aij(j,i)=a
195 a=.5*a
196 a14(i,j)=a
197 a14(j,i)=a
198 enddo
199 do(i)=do_s(i)
200 ac(i)=ac_s(i)
201 enddo
202
[bd2278d]203! +++++++++++++++++++++++++++++++++
[e40e335]204 cij(1,1)=45.5d0
205 aij(1,1)=14090.0d0
206 cij(2,2)=45.5d0
207 aij(2,2)=14380.0d0
208 cij(3,3)=45.5d0
209 aij(3,3)=8420.0d0
210 cij(4,4)=45.5d0
211 aij(4,4)=8420.0d0
212 cij(5,5)=45.5d0
213 aij(5,5)=11680.0d0
214 cij(6,6)=45.5d0
215 aij(6,6)=14380.0d0
216 cij(7,7)=370.5d0
217 aij(7,7)=906100.0d0
218 cij(8,8)=766.6d0
219 aij(8,8)=1049000.0d0
220 cij(9,9)=509.5d0
221 aij(9,9)=653600.0d0
222 cij(10,10)=217.2d0
223 aij(10,10)=125600.0d0
224 cij(11,11)=369.0d0
225 aij(11,11)=170200.0d0
226 cij(12,12)=217.2d0
227 aij(12,12)=125600.0d0
228 cij(13,13)=401.3d0
229 aij(13,13)=375200.0d0
230 cij(14,14)=401.3d0
231 aij(14,14)=375200.0d0
232 cij(15,15)=401.3d0
233 aij(15,15)=375200.0d0
234 cij(16,16)=2274.4d0
235 aij(16,16)=5809000.0d0
236 cij(17,17)=45.5d0
237 aij(17,17)=5340.0d0
238 cij(18,18)=370.5d0
239 aij(18,18)=909000.0d0
[bd2278d]240! +++++++++++++++++++++++++++++++++
[e40e335]241 do i=1,mxtyat
242 a14(i,i)=.5*aij(i,i)
243 enddo
[bd2278d]244! +++++++++++++++++++++++++++++++++
[e40e335]245
246 do i=1,mxtyat
[bd2278d]247! write( *, '(18f14.6)' ) ( a14(i,j), j = 1, mxtyat )
[e40e335]248 enddo
249
250 do i=1,mxhbdo
251 do j=1,mxhbac
252 hbc(i,j)=chb_s(i,j)
253 hba(i,j)=ahb_s(i,j)
254 enddo
255 enddo
256
257 do i=1,mxtyto
258 e0to(i)=e0to_s(i)/2.
259 sgto(i)=sgto_s(i)
260 rnto(i)=rnto_s(i)
261 enddo
262
263
264 endif
[bd2278d]265! -------------------------------------------- Hydrogen Bond Parameters
[e40e335]266 do i=1,mxtyat
267 do j=1,mxtyat
268 ihbty(i,j)=0
269 chb(i,j)=0.
270 ahb(i,j)=0.
271 enddo
272 enddo
273
274 iac=0
275 ido=0
276 do i=1,mxtyat
277 if (do(i)) then
278 ido=ido+1
279 jac=0
280 do j=1,i-1
281 if (ac(j)) then
282 jac=jac+1
283 ihbty(i,j)=1
284 ihbty(j,i)=-1
285 chb(i,j)=hbc(ido,jac)
286 chb(j,i)=chb(i,j)
287 ahb(i,j)=hba(ido,jac)
288 ahb(j,i)=ahb(i,j)
289 endif
290 enddo
291 elseif (ac(i)) then
292 iac=iac+1
293 jdo=0
294 do j=1,i-1
295 if (do(j)) then
296 jdo=jdo+1
297 ihbty(i,j)=-1
298 ihbty(j,i)=1
299 chb(i,j)=hbc(jdo,iac)
300 chb(j,i)=chb(i,j)
301 ahb(i,j)=hba(jdo,iac)
302 ahb(j,i)=ahb(i,j)
303 endif
304 enddo
305 endif
306 enddo
307
308 do i=1,mxtyto ! eases calculation of torsional derivatives
309 esnto(i)=e0to(i)*sgto(i)*rnto(i)
310 enddo
311
312 return
313 end
[bd2278d]314! **************
[e40e335]315 BLOCK DATA
316
317 include 'INCL.H'
[32289cd]318
319 integer i
[e40e335]320
[bd2278d]321! Atom types ------------------------------------------------------------
322! Original types -Scheraga: -Flex:
323! H 1 - with aliphatic carbon 1 12
324! 2 - with aromatic carbon 3 13
325! 3 - with non-sp3 types of nitrogen 2 1
326! 4 - with sp3-hybr. nitrogen 2 2
327! 5 - with oxygen 4 1
328! 6 - with sulfur 3(was 5)1
329! C 7 - sp3-hybr. carbon 6,9 3
330! 8 - sp2-carbon (carbonyl,carboxyl,carboxylate) 7,11 4
331! 9 - aromatic carbon 8,10 4
332! O 10 - hydroxyl, ester oxygen (inc. water) 18,19 8
333! 11 - carbonyl oxygen 17 9
334! 12 - carboxylate oxygen 18,19 10
335! N 13 - aliph. nitrogen with 0/1 hydrogen & charged N 13-15 6
336! 14 - nitrogen with two hydrogens 13-15 5
337! 15 - all other nitrogens (+ sp2-hybrid. in heteroc.) 13-15 7
338! S 16 - any sulfur 20,21 18,19
339! H 17 - H-delta of Pro, Hyp of ECEPP/3 dataset 5(new) -
340! C 18 - C-delta of Pro, Hyp of ECEPP/3 dataset 12(new) -
341
342! Classes for torsional potential ---------------------------------------
343!
344! 1 : 'Omega' = C'(pept.)-N(pept.) [Cpept-Npept]
345! 2 : 'Phi' = N(pept.)-C(sp3) [C4-Npept]
346! 3 : 'Psi' = C(sp3)-C'(pept.) [C4-Cpept]
347! 4 : 'Chi1' = C(sp3)-C(sp3) [C4-C4]
348! 5 : C(sp3)-OH (Hydroxyl) [C4-OH]
349! 6 : C(sp3)-NH2 [C4-NH2]
350! 7 : C(sp3)-NH3+ [C4-NH3+]
351! 8 : C(sp3)-NH-(guanidyl) [C4-NHX]
352! 9 : C(sp3)-COOH(carboxyl) [C4-COO]
353! 10 : C(sp3)-COO-(carboxylate) [C4-COO]
354! 11 : C(sp3)-CO(sp2 of amide) [C4-Cpept]
355! 12 : C(sp3)-C(aromatic ring) [C4-C3]
356! 13 : C(sp3)-S [C4-SC4]
357! 14 : C(sp3)-SH [C4-SH]
358! 15 : C(aromatic ring)-OH [C3-OH]
359! ________________________________________________ "rigid" torsions:
360! 16 : C(carboxyl)-OH [C3-OH]
361! 17 : -NH-C(sp2 of guanidyl) [C3-NHX]
362! 18 : -C(sp3)-NH2 (guanidyl) [not in Flex]
363! 19 : -C(sp3)-NH2 (amide) [Cpept-Npept]
[e40e335]364
365 data conv/332.d0/ ! to convert electrost. energy into [kcal/mole]
366
[bd2278d]367! ------------------------- ECEPP/3 potential --------------------------------
368! 1) Momany F.A McGuire R.F Burgess A.W Scheraga H.A J Phys Chem v79 2361-2381
369! 1975
370! 2) Nemethy G Pottle M.S Scheraga H.A, J Phys Chem v87 1883-1887 1983
371! 3) Sippl M.J Nemethy G Scheraga H.A J Phys Chem v88 6231-6233 1984
372! 4) Nemethy G Gibson K.D Palmer K.A Yoon C.N Paterlini G Zagari A Rumsey S
373! Scheraga H.A J Phys Chem v96 6472-6484 1992
374! ----------------------------------------------------------------------------
[e40e335]375
376 data eps_s/2.d0/ ! Distance-INdependent diel. constant
[bd2278d]377! data eps_s/6.d0/ ! Distance-INdependent diel. constant
[e40e335]378 data plt/78.d0/, slp/0.3d0/ ! Parameters for Epsilon(R)
379
380 data ehm /362.55d0/ ! Angstrom**2/3 * kcal / mol ! from KONF90
[bd2278d]381! data ehm /362.09561409d0/ ! Angstrom**2/3 * kcal / mol
382! From:
383! 1.5
384! * elementary charge = 4.80325 *e+2 Angstrom**3/2 * g**1/2 * s**(-1)
385! * Planck's constant/2*Pi = 1.0545887 *e-34 Joule * s
386! * Avogadro's number = 6.022045 *e+23 mol**(-1)
387! / sqrt (mass of electron) = sqrt (9.109534 *e-28 g )
388! / thermal equivalent = 4.1868 *e+3 Joule * kcal**(-1)
389! data ehm /362.36d0/ ! calculated using Tab II in ref. 2
390! data 1/ehm /2.757670d-3/ ! 3*sqrt(m)/(2*e*h) taken from ICM
391
392! ---------------------- atomic polarizabilties (*100,[Angstrom**3])
393! 1 2 3 4 5 6 7 8 9 10 11 12
[e40e335]394 data atpl/42.,42.,42.,42.,42.,42.,93.,151.,115.,59.,84.,59.,
[bd2278d]395! 13 14 15 16 17 18
396 & 93.,93.,93.,220.,42.,93./
397! ---------------------- effective numbers of electrons (*100,ref. 2)
398! 1 2 3 4 5 6 7 8 9 10 11 12
[e40e335]399 data efel/85.,85.,85.,85.,85.,85.,520.,520.,520.,700.,700.,700.,
[bd2278d]400! 13 14 15 16 17 18
401 & 610.,610.,610.,1480.,85.,520./
402! ------------------------- min. pairwise 6-12 energy (*1000,[kcal/mol])
403! 1 2 3 4 5 6 7 8 9 10 11 12
[e40e335]404 data emin/37.,36.,61.,61.,44.,36.,38.,140.,99.,94.,200.,94.,
[bd2278d]405! 13 14 15 16 17 18
406 & 107.,107.,107.,223.,99.,38./
407! ---------------------------- opt. pairwise distance (*100,[Angstrom])
408! 1 2 3 4 5 6 7 8 9 10 11
[e40e335]409 data rmin/292.,293.,268.,268.,283.,293.,412.,374.,370.,324.,312.,
[bd2278d]410! 12 13 14 15 16 17 18
411 & 324.,351.,351.,351.,415.,248.,412./
412! ---------------------------------------------- Hydrogen-bond donors
413! 1 2 3 4 5 6
[e40e335]414 data do_s/.false.,.false.,.true.,.true.,.true.,.false.,
[bd2278d]415! 7 8 9 10 11 12
416 & .false.,.false.,.false.,.false.,.false.,.false.,
417! 13 14 15 16 17 18
418 & .false.,.false.,.false.,.false.,.false.,.false./
419! -------------------------------------------- Hydrogen-bond acceptors
420! 1 2 3 4 5 6
[e40e335]421 data ac_s/.false.,.false.,.false.,.false.,.false.,.false.,
[bd2278d]422! 7 8 9 10 11 12
423 & .false.,.false.,.false.,.true.,.true.,.true.,
424! 13 14 15 16 17 18
425 & .true.,.true.,.true.,.false.,.false.,.false./
426! & .false.,.true.,.true.,.false.,.false.,.false./ !! ICM
427! --------------------------------- HB-parameters (/1000,attraction)
[e40e335]428 data chb_s/2624.,2624.,4610.,.0, ! given as:
[bd2278d]429 & 4014.,4014.,5783.,.0, ! (ac_typ x do_typ)
430 & 2624.,2624.,4610.,.0, ! to be used:
431 & 8244.,8244.,8244.,.0, ! (DO_typ x AC_typ)
432 & 8244.,8244.,8244.,.0, ! i.e.:
433 & 8244.,8244.,8244.,.0/ ! ( 3-5 x 10-15 )
434! --------------------------------- HB-parameters (/1000,repulsion)
[e40e335]435 data ahb_s/ 5890., 5890.,11220.,.0,
[bd2278d]436 & 12040.,12040.,16583.,.0, ! 13344 -> 16583 = Ref. 3
437 & 5890., 5890.,11220.,.0,
438 & 32897.,32897.,32897.,.0,
439 & 32897.,32897.,32897.,.0,
440 & 32897.,32897.,32897.,.0/
[e40e335]441
[bd2278d]442! 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
[e40e335]443 data e0to_s /20.,0.,0.,2.7,.6,1.8,1.8,0.,0.,0.,0.,0.,2.,1.5,3.5
[bd2278d]444! 16 17 18 19
445 & ,8.,18.,20.,15./
[e40e335]446 data sgto_s /-1.,0.,0., 1.,1., 1., 1.,0.,0.,0.,0.,0.,1., 1.,-1.
[bd2278d]447 & ,-1.,-1.,-1.,-1./
[e40e335]448 data rnto_s / 2.,0.,0., 3.,3., 3., 3.,0.,0.,0.,0.,0.,3., 3., 2.
[bd2278d]449 & ,2., 2., 2., 2./
[e40e335]450
[bd2278d]451! ---------------------------- Flex potential ----------------------------------
452! Lavery R Sklenar H Zakrzewska K Pullman B J Biomol Struct Dyn v3 989-1014 1986
453! VdW-parameters from: Zhurkin V.B Poltiev V.I Florent'ev V.L Molekulyarnaya
454! Biologiya v14 116 1980
455! ------------------------------------------------------------------------------
[e40e335]456
457 data plt_f/78.d0/, slp_f/0.16d0/ ! Parameters for Epsilon(R)
458 data cohb_f/6.d0/ ! Cut-off distance betw. H- & acceptor atom for HB
459 data c_f/ ! ----------- Lennard-Jones C6-parameters (attraction)
[bd2278d]460 &40.,40.,40.,40.,40.,40.,100.,126.,126.,86.,121.,105.,126.,105.,
461 &146.,213.1,3*0.,40.,40.,40.,40.,40.,100.,126.,126.,86.,121.,105.,
462 &126.,105.,146.,213.1,4*0.,40.,40.,40.,40.,100.,126.,126.,86.,121.,
463 &105.,126.,105.,146.,213.1,5*0.,40.,40.,40.,100.,126.,126.,86.,121.
464 &,105.,126.,105.,146.,213.1,6*0.,40.,40.,100.,126.,126.,86.,121.,
465 &105.,126.,105.,146.,213.1,7*0.,40.,100.,126.,126.,86.,121.,105.,
466 &126.,105.,146.,213.1,8*0.,250.,316.,316.,217.,305.,264.,316.,264.,
467 &367.,489.,9*0.,400.,400.,274.,385.,334.,400.,334.,464.,537.4,10*0.
468 &,400.,274.,385.,334.,400.,334.,464.,537.4,11*0.,200.,283.,245.,
469 &278.,233.,330.,424.,12*0.,400.,347.,391.,327.,465.,583.,13*0.,300.
470 &,339.,284.,403.,530.,14*0.,400.,334.,467.,556.5,15*0.,280.,391.,
471 &484.,16*0.,550.,673.4,17*0.,246.,38*0./
[e40e335]472 data a_f/ ! ---- Lennard-Jones A12-parameters (/1000,repulsion)
[bd2278d]473 &7.74,7.74,7.74,7.74,7.74,7.74,70.6,81.6,81.6,31.3,42.2,36.6,71.4,
474 &62.,78.3,189.3,3*0.,7.74,7.74,7.74,7.74,7.74,70.6,61.7,61.7,31.3,
475 &17.8,15.4,53.7,62.,58.7,189.3,4*0.,7.74,7.74,7.74,7.74,70.6,81.6,
476 &81.6,31.3,42.2,36.6,71.4,62.,78.3,189.3,5*0.,7.74,7.74,7.74,70.6,
477 &61.7,61.7,31.3,17.8,15.4,53.7,62.,58.7,189.3,6*0.,7.74,7.74,70.6,
478 &81.6,81.6,31.3,42.2,36.6,71.4,62.,78.3,189.3,7*0.,7.74,70.6,81.6,
479 &81.6,31.3,42.2,36.6,71.4,62.,78.3,189.3,8*0.,512.,601.,601.,256.,
480 &349.,302.,538.,464.,598.,1196.,9*0.,704.,704.,298.,406.,351.,630.,
481 &544.,699.,1203.5,10*0.,704.,298.,406.,351.,630.,544.,699.,1203.5,
482 &11*0.,129.,176.,153.,269.,233.,303.,561.8,12*0.,240.,208.,366.,
483 &317.,413.,772.5,13*0.,180.,317.,274.,358.,702.3,14*0.,565.,488.,
484 &629.,1105.8,15*0.,421.,544.,976.8,16*0.,705.,1259.5,17*0.,503.3,
485 &38*0./
486! ---------------------------------------------- Hydrogen-bond donors
487! 1 2 3 4 5 6
[e40e335]488 data do_f/.false.,.false.,.true.,.true.,.true.,.true.,
[bd2278d]489! 7 8 9 10 11 12
490 & .false.,.false.,.false.,.false.,.false.,.false.,
491! 13 14 15 16 17 18
492 & .false.,.false.,.false.,.false.,.false.,.false./
493! -------------------------------------------- Hydrogen-bond acceptors
494! 1 2 3 4 5 6
[e40e335]495 data ac_f/.false.,.false.,.false.,.false.,.false.,.false.,
[bd2278d]496! 7 8 9 10 11 12
497 & .false.,.false.,.false.,.true.,.true.,.true.,
498! 13 14 15 16 17 18
499 & .false.,.false.,.true.,.true.,.false.,.false./
500! --------------------------------- HB-parameters (/1000,attraction)
[e40e335]501 data chb_f/180.,180.,160. ,226.8, ! given as (ac_typ x do_typ)
[bd2278d]502 & 175.,175.,150. ,305.8, ! to be used as:
503 & 100.,100., 85. , 85. , ! (Do_typ x Ac_typ)
504 & 165.,165.,150. ,305.8, ! i.e.:
505 & 720.,720.,643.1,845.6, ! ( 3-6 x 10-12,15,16 )
506 & 0., 0., 0. , 0. /
507! --------------------------------- HB-parameters (/1000,repulsion)
[e40e335]508 data ahb_f/ 6600., 6600., 6200., 12855.,
[bd2278d]509 & 6400., 6400., 7100., 29216.,
510 & 2400., 2400., 2400., 2000.,
511 & 6200., 6200., 7100., 29216.,
512 & 185000.,185000.,172301.,308235.,
513 & 0., 0., 0., 0./
[e40e335]514
[bd2278d]515! 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
[e40e335]516 data e0to_f /20.,2.,.8,2.6,.6,2.1,1.8,3.2,.5,.5,.8,1.2,1.3,1.,6.2
[bd2278d]517! 16 17 18 19
518 & ,6.2, 8.,0.,20./
[e40e335]519 data sgto_f /-1.,1.,-1., 1.,1., 1., 1.,1.,1.,1.,-1.,1., 1.,1.,-1.
[bd2278d]520 & ,-1.,-1.,0.,-1./
[e40e335]521 data rnto_f / 2.,3., 3., 3.,3., 6., 3.,3.,6.,6., 3.,6., 3.,3., 2.
[bd2278d]522 & ,2., 2.,0.,2./
[e40e335]523
524 data (rsnmcd(i),i=1,nrsty)/ ! Names for all amino acid residue types
[bd2278d]525 & 'ala ','arg ','arg+','asn ','asp ','asp-','cys ','cyss','gln ',
526 & 'glu ','glu-','gly ','his ','hise','hisd','his+','hyp ','hypu',
527 & 'ile ','leu ','lys ','lys+','met ','phe ','cpro','pro ','cpru',
528 & 'prou','pron','pro+','ser ','thr ','trp ','tyr ','val ' /
[32289cd]529
[e40e335]530 data (onltcd(i),i=1,nrsty)/ ! One-letter codes for amino acid types
[bd2278d]531 & 'A', 'R', 'R', 'N', 'D', 'D', 'C', 'C', 'Q',
532 & 'E', 'E', 'G', 'H', 'H', 'H', 'H', 'P', 'P',
533 & 'I', 'L', 'K', 'K', 'M', 'F', 'P', 'P', 'P',
534 & 'P', 'P', 'P', 'S', 'T', 'W', 'Y', 'V' /
535
536! The vdW radii (in Angstr.) for the atomic groups and
537! coefficients for their solvation free energy (kcal/molxA**2)
538
[32289cd]539! Method:
[bd2278d]540
[32289cd]541! itysol=1 : OONS --> T.Ooi, et al,
[bd2278d]542! Proc. Natl. Acad. Sci. USA 8 (1987) 3086-3090.
[32289cd]543! itysol=2 : JRF --> J.Vila, et al,
[bd2278d]544! PROTEINS: Struct Funct Genet 10(1991) 199-218.
[32289cd]545! itysol=3 : WE92 --> L.Wesson, D.Eisenberg,
[bd2278d]546! Protein Science 1 (1992) 227-235.
547! itysol=4 : SCH1 --> D.Eisenberg, et al,
548! Chem Scrip 29A (1989) 217-221.
549! itysol=5 : SCH2 --> A.H.Juffer, et al,
550! Proteine Science 4 (1995) 2499-2509.
[32289cd]551! itysol=6 : SCH3 --> L.Wesson, D.Eisenberg,
[bd2278d]552! Protein Science 1 (1992) 227-235.
553! itysol=7 : SCH4 --> C.A. Schiffer, et al,
554! Mol. Simul. 10(1993) 121-149.
[32289cd]555! itysol=8 : EM86 --> D.Eisenberg, A.D. Mclachlan,
[bd2278d]556! Nature 319 (1986) 199-203.
557! itysol=9 : BM --> B. Freyberg, et al,
558! J. Mol. Biol. 233 (1993) 275-292.
559
560! ATOM
561! TYPE OONS JRF WE92 SCH1 SCH2 SCH3 SCH4 EM86 BM
562
563! 1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.000 0.000
564! 2 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.000 0.000
565! 3 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.000 0.000
566! 4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.000 0.000
567! 5 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.000 0.000
568! 6 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.000 0.000
569! 7 0.0080 0.2160 0.0120 0.0180 0.0130 0.0040 0.0325 0.016 1.000
570! 8 0.4270 -0.7320 0.0120 0.0180 0.0130 0.0040 0.0325 0.016 1.000
571! 9 -0.0080 -0.6780 0.0120 0.0180 0.0130 0.0040 0.0325 0.016 1.000
572!10 -0.1720 -0.9100 -0.1160 -0.0090 -0.0070 -0.1130 -0.0175 -0.006 0.000
573!11 -0.0380 -0.2620 -0.1750 -0.0090 -0.0070 -0.1660 -0.2800 -0.006 0.000
574!12 -0.0380 -0.9100 -0.1750 -0.0370 -0.1120 -0.1660 -0.2800 -0.024 0.000
575!13 -0.1320 -0.3120 -0.1860 -0.0380 -0.0870 -0.1690 -0.2175 -0.05 0.000
576!14 -0.1320 -0.3120 -0.1160 -0.0090 -0.0070 -0.1130 -0.0175 -0.006 0.000
577!15 -0.1320 -0.3120 -0.1160 -0.0090 -0.0070 -0.1130 -0.0175 -0.006 0.000
578!16 -0.0210 -0.2810 -0.0180 0.0050 -0.0036 -0.0170 -0.0090 0.021 0.000
579!17 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.000 0.000
580!18 0.0080 0.2160 0.0120 0.0180 0.0130 0.0040 0.0325 0.016 1.000
[e40e335]581
582 data coef_sl/54*0.0,
[bd2278d]583 & 0.008, 0.216, 0.012, 0.018, 0.013, 0.004, 0.0325, 0.016,1.000,
584 & 0.427,-0.732, 0.012, 0.018, 0.013, 0.004, 0.0325, 0.016,1.000,
585 & -.008,-0.678, 0.012, 0.018, 0.013, 0.004, 0.0325, 0.016,1.000,
586 & -.172,-0.910,-0.116,-0.009,-0.007,-0.113,-0.0175,-0.006,0.000,
587 & -.038,-0.262,-0.116,-0.009,-0.007,-0.113,-0.0175,-0.006,0.000,
588 & -.038,-0.910,-0.175,-0.037,-0.112,-0.166,-0.2800,-0.024,0.000,
589 & -.132,-0.312,-0.186,-0.038,-0.087,-0.169,-0.2175,-0.05, 0.000,
590 & -.132,-0.312,-0.116,-0.009,-0.007,-0.113,-0.0175,-0.006,0.000,
591 & -.132,-0.312,-0.116,-0.009,-0.007,-0.113,-0.0175,-0.006,0.000,
592 & -.021,-0.281,-0.018, 0.005,-.0036,-0.017,-0.0090, 0.021,0.000,
593 & 9*0.0,
594 & 0.008, 0.216, 0.012, 0.018, 0.013, 0.004, 0.0325, 0.016,1.000/
[e40e335]595
596 data rad_vdw/54*0.,
[bd2278d]597 & 2*2.0,6*1.9,2.0,
598 & 2*1.55,6*1.9,1.5,
599 & 2*1.75,6*1.9,1.85,
600 & 9*1.4,
601 & 9*1.4,
602 & 9*1.4,
603 & 2*1.55,6*1.7,1.5,
604 & 2*1.55,6*1.7,1.5,
605 & 2*1.55,6*1.7,1.5,
606 & 2*2.0,6*1.8,1.85,
607 & 9*0.,
608 & 2*2.0,6*1.9,2.0/
[e40e335]609
610 end
611
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