Fw: [gmx-users] position restraints
Shima Arasteh
shima_arasteh2001 at yahoo.com
Tue Mar 26 19:20:39 CET 2013
The inclusion part was edited again in original top file. I dont know why I had written that! Sorry.
But about last itp files, which you mentioned that they are created incorrectly, 1) I 'd like to know what itp file should be created? In my own, I just included the chain_B.itp file with the same numbering as the chain_A.itp file.
2) One more thing, restraints for both chains are brought just one time in the processed.top file? I thought after each chain, the restraints which are included should be brought and written in processed.top file!!!
With these modifications, I got this top file:
;
; File 'topol.top' was generated
; By user: shima (1000)
; On host: linux-cbyo.site
; At date: Wed Dec 12 12:17:51 2012
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.5
;
; Command line was:
; pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p
;
; Force field was read from current directory or a relative path - path added.
;
; Include forcefield parameters
; Conversion of CHARMM36 parameters to GROMACS format by Thomas Piggot, July 2010.
; Also added some parameters from later CHARMM27 versions, such as those for the PS headgroup.
;
; If you use these parameters please check out the forcefield.doc for papers to cite
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
;
; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and CCL) - Thomas Pigot July 2010
;
[ atomtypes ]
;name at.num mass charge ptype sigma epsilon
C 6 12.01100 0.51 A 0.356359487256 0.46024
.
.
.
OBL OHL 1 0.28241489365 0.565258245152
OBL OSL 1 0.271724109033 0.45833423612 ; Different to C27
OBL OSLP 1 0.271724109033 0.45833423612 ; Not in C27
OBL NH3L 1 0.289542083396 0.648182492821
OBL NTL 1 0.289542083396 0.648182492821
OBL SL 1 0.311814551349 0.993644945843
OBL PL 1 0.316269044939 1.10856262394
;
; Added new and changed old bonds/angles/dihedrals/impropers for CHARMM36 Lipids and also PS headgroup - Thomas Piggot July 2010
;
; Also added in (but commented out) parameters for a trans double bond - TJP July 2010
;
[ bondtypes ]
; i j func b0 kb
C HA 1 0.110 261568.824! FORM, formamide reverted to value from par_all22_prot.inp and par_cgenff_1d.inp
CST OST 1 0.116 784884.928
SS FE 1 0.232 209200.0
C C 1 0.1335 502080.0
CA CA 1 0.1375 255224.0
.
.
.
X FE NPH X 9 0.00 0.0 2
; ### For Heme bound to HSD
; Charmm patch PHEM defines only one dihedral term: 1CD2 1NE2 2FE 2NA
; (1 = HSD, 2 = HEME)
; In gromacs we cannot differentiate between NA, NB, NC, and ND of the heme.
; (values cannot be attributed in the rtp file for dihedrals involving atoms
; from other residues)
; So we divide the original force constant (0.2092) by four.
NPH FE NR2 CPH1 9 0.00 0.0 4 ; This one is always zero.
NPH FE NR2 CPH2 9 0.00 0.0523 4 ; This is X-FE-NR2-X from charmm
FE NR2 CPH1 X 9 0.00 0.0 1
FE NR2 CPH2 X 9 0.00 0.0 1
; ### For Heme bound to O2 or CO, we dont have to do this trick, because the force constant is 0.0
X FE OM X 9 0.00 0.0 4
OM FE NR2 X 9 0.00 0.0 1
CM FE NR2 X 9 0.00 0.0 1
; ###
X NPH CPA X 9 0.00 0.0 2
X CTL1 OHL X 9 0.00 0.58576 3
X CTL2 OHL X 9 0.00 0.58576 3
X CTL3 OHL X 9 0.00 0.58576 3
.
.
.
.
X CEL1 CEL1 X 9 180.00 1.8828 1 ; New
X CEL1 CEL1 X 9 180.00 35.564 2
X CEL2 CEL2 X 9 180.00 20.5016 2
[ dihedraltypes ]
; i j k l func q0 cq
C NH1 O HA 2 0.00 66.0000 ! J8_FVAL- , from CG2O1 NG2S2 OG2D1 HGR52, penalty= 1V
CPB CPA NPH CPA 2 0.0000 174.0544
HA CPA CPA CPM 2 0.0000 246.0192
HE2 HE2 CE2 CE2 2 0.00 25.104
HR1 NR1 NR2 CPH2 2 0.0000 4.184
HR1 NR2 NR1 CPH2 2 0.0000 4.184
HR3 CPH1 NR1 CPH1 2 0.0000 4.184
HR3 CPH1 NR2 CPH1 2 0.0000 4.184
; Include chain topologies
;
; File 'topol_Protein_chain_A.itp' was generated
; By user: shima (1000)
; On host: linux-cbyo.site
; At date: Wed Dec 12 12:17:55 2012
;
; This is a include topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.5
;
; Command line was:
; pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p
;
; Force field was read from current directory or a relative path - path added.
;
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 FVAL rtp FVAL q 0.0
1 C 1 FVAL CN 1 0.357 12.011 ; qtot 0.357
2 HA 1 FVAL H1 2 0.1 1.008 ; qtot 0.457
3 O 1 FVAL ON 3 -0.51 15.999 ; qtot -0.053
4 NH1 1 FVAL N 4 -0.423 14.007 ; qtot -0.476
5 H 1 FVAL HN 5 0.333 1.008 ; qtot -0.143
.
.
.
.
357 HB 24 GLY HA2 357 0.09 1.008 ; qtot 2
358 CC 24 GLY C 358 0.34 12.011 ; qtot 2.34
359 OC 24 GLY OT1 359 -0.67 15.999 ; qtot 1.67
360 OC 24 GLY OT2 360 -0.67 15.999 ; qtot 1
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
.
.
.
353 351 355 354 2
358 355 360 359 2
[ cmap ]
; ai aj ak al am funct
18 20 22 29 31 1
29 31 33 48 50 1
48 50 52 55 57 1
55 57 59 74 76 1
74 76 78 85 87 1
85 87 89 104 106 1
104 106 108 114 116 1
114 116 118 134 136 1
134 136 138 145 147 1
145 147 149 161 163 1
161 163 165 171 173 1
171 173 175 187 189 1
187 189 191 198 200 1
198 200 202 217 219 1
217 219 221 227 229 1
227 229 231 251 253 1
251 253 255 262 264 1
262 264 266 282 284 1
282 284 286 292 294 1
292 294 296 316 318 1
316 318 320 327 329 1
327 329 331 351 353 1
; Include Position restraint file
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
3 1 1000 1000 1000
4 1 1000 1000 1000
6 1 1000 1000 1000
.
.
.
348 1 1000 1000 1000
351 1 1000 1000 1000
352 1 1000 1000 1000
353 1 1000 1000 1000
355 1 1000 1000 1000
358 1 1000 1000 1000
359 1 1000 1000 1000
360 1 1000 1000 1000
; position restraints for a_1-360 of Protein
[ position_restraints ]
; i funct fcx fcy fcz
1 1 100000 100000 100000
2 1 100000 100000 100000
3 1 100000 100000 100000
4 1 100000 100000 100000
5 1 100000 100000 100000
6 1 100000 100000 100000
7 1 100000 100000 100000
8 1 100000 100000 100000
9 1 100000 100000 100000
10 1 100000 100000 100000
11 1 100000 100000 100000
12 1 100000 100000 100000 .
.
.
.
345 1 100000 100000 100000
346 1 100000 100000 100000
347 1 100000 100000 100000
348 1 100000 100000 100000
349 1 100000 100000 100000
350 1 100000 100000 100000
351 1 100000 100000 100000
352 1 100000 100000 100000
353 1 100000 100000 100000
354 1 100000 100000 100000
355 1 100000 100000 100000
356 1 100000 100000 100000
357 1 100000 100000 100000
358 1 100000 100000 100000
359 1 100000 100000 100000
360 1 100000 100000 100000
;
; File 'topol_Protein_chain_B.itp' was generated
; By user: shima (1000)
; On host: linux-cbyo.site
; At date: Wed Dec 12 12:17:57 2012
;
; This is a include topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.5
;
; Command line was:
; pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p
;
; Force field was read from current directory or a relative path - path added.
;
[ moleculetype ]
; Name nrexcl
Protein_chain_B 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 FVAL rtp FVAL q 0.0
1 C 1 FVAL CN 1 0.357 12.011 ; qtot 0.357
2 HA 1 FVAL H1 2 0.1 1.008 ; qtot 0.457
3 O 1 FVAL ON 3 -0.51 15.999 ; qtot -0.053
.
.
.
354 H 24 GLY HN 354 0.31 1.008 ; qtot 1.84
355 CT2 24 GLY CA 355 -0.02 12.011 ; qtot 1.82
356 HB 24 GLY HA1 356 0.09 1.008 ; qtot 1.91
357 HB 24 GLY HA2 357 0.09 1.008 ; qtot 2
358 CC 24 GLY C 358 0.34 12.011 ; qtot 2.34
359 OC 24 GLY OT1 359 -0.67 15.999 ; qtot 1.67
360 OC 24 GLY OT2 360 -0.67 15.999 ; qtot 1
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
4 5 1
4 6 1
6 7 1
.
.
.
316 318 320 327 329 1
327 329 331 351 353 1
; Include Position restraint file
; position restraints for a_360-720 of Protein
[ position_restraints ]
; i funct fcx fcy fcz
1 1 100000 100000 100000
2 1 100000 100000 100000
3 1 100000 100000 100000
4 1 100000 100000 100000
5 1 100000 100000 100000
6 1 100000 100000 100000
7 1 100000 100000 100000
8 1 100000 100000 100000
9 1 100000 100000 100000
10 1 100000 100000 100000
11 1 100000 100000 100000
12 1 100000 100000 100000
13 1 100000 100000 100000
14 1 100000 100000 100000
15 1 100000 100000 100000
16 1 100000 100000 100000
17 1 100000 100000 100000
18 1 100000 100000 100000
19 1 100000 100000 100000
20 1 100000 100000 100000
21 1 100000 100000 100000
22 1 100000 100000 100000
23 1 100000 100000 100000
24 1 100000 100000 100000
25 1 100000 100000 100000
26 1 100000 100000 100000
27 1 100000 100000 100000
28 1 100000 100000 100000
29 1 100000 100000 100000
30 1 100000 100000 100000
.
.
.
354 1 100000 100000 100000
355 1 100000 100000 100000
356 1 100000 100000 100000
357 1 100000 100000 100000
358 1 100000 100000 100000
359 1 100000 100000 100000
360 1 100000 100000 100000
; Include POPC chain topology
[ moleculetype ]
; Name nrexcl
POPC 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 POPC rtp POPC q 0.0
1 NTL 1 POPC N 1 -0.6 14.007 ; qtot -0.6
2 CTL2 1 POPC C12 2 -0.1 12.011 ; qtot -0.7
3 CTL5 1 POPC C13 3 -0.35 12.011 ; qtot -1.05
4 CTL5 1 POPC C14 4 -0.35 12.011 ; qtot -1.4
5 CTL5 1 POPC C15 5 -0.35 12.011 ; qtot -1.75
6 HL 1 POPC H12A 6 0.25 1.008 ; qtot -1.5
129 128 131 134 9
130 128 131 132 9
130 128 131 133 9
130 128 131 134 9
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
31 30 33 32 2
40 39 42 41 2
; position restraints for TOM_TYPE_P of Protein
[ position_restraints ]
; i funct fcx fcy fcz
20 1 100000 100000 100000
; Include water topology
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 OWT3 1 SOL OW 1 -0.834
2 HWT3 1 SOL HW1 1 0.417
3 HWT3 1 SOL HW2 1 0.417
[ settles ]
; i j funct length
1 1 0.09572 0.15139
[ exclusions ]
1 2 3
2 1 3
3 1 2
; Include topology for ions
[ moleculetype ] ; added by Bjelkmar Jan 2010, from c32b1/toppar/stream/toppar_water_ions.str
; molname nrexcl
OH 1
[ atoms ]
; id at type res nr residu name at name cg nr charge mass
1 OC 1 OH O1 1 -1.32
2 H 1 OH H1 1 0.32
[ bonds ]
;i j funct length force.c.
1 2 1 0.09700 456056 ; hydroxyl bond
[ moleculetype ]
; molname nrexcl
NA 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 SOD 1 NA NA 1 1
[ moleculetype ]
; molname nrexcl
MG 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 MG 1 MG MG 1 2
[ moleculetype ]
; molname nrexcl
K 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 POT 1 K K 1 1
[ moleculetype ]
; molname nrexcl
Ces 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 CES 1 Ces Ces 1 1
[ moleculetype ]
; molname nrexcl
Cal 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 CAL 1 Cal Cal 1 2
[ moleculetype ]
; molname nrexcl
CL 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 CLA 1 CL CL 1 -1
[ moleculetype ]
; molname nrexcl
ZN 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 ZN 1 ZN ZN 1 -2
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
POPC 238
SOL 18706
NA 615
CL 617
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc:
Sent: Tuesday, March 26, 2013 9:55 PM
Subject: Re: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:
>
>
>
> Have a look at processed topology file here please; I see that position
> restraints are brought after chain_A but not brought after chain_B.
>
> With these settings:
> ; Include chain topologies
> #ifdef POSRES
> #include "topol_Protein_chain_A.itp"
> #include "protein_chain_A_posre.itp"
> #endif
> #ifdef POSRES
> #include "topol_Protein_chain_B.itp"
> #include "protein_chain_B_posre.itp"
> #endif
>
>
The above approach is incorrect. The inclusion of protein topologies is
dependent upon using position restraints? That's certainly not right,
especially if you ever want to run a simulation without restraints. The
following is the correct approach:
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "protein_chain_A_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "protein_chain_B_posre.itp"
#endif
Also adding "define = -DPOSRES_LIPID -DPOSRES ", I get this processed.top:
>
>
> #grompp -f nvt.mdp -c minim.gro -p topol.top -n index.ndx -o nvt.tpr -pp
>
> THIS IS THE PROCESSED TOPOLOGY:
> ; File 'topol.top' was generated
> ; By user: shima (1000)
> ; On host: linux-cbyo.site
> ; At date: Wed Dec 12 12:17:51 2012
> ;
> ; This is a standalone topology file
> ;
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.5.5
> ;
> ; Command line was:
> ; pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p
> ;
> ; Force field was read from current directory or a relative path - path
> added.
> ;
>
> ; Include forcefield parameters
> ; Conversion of CHARMM36 parameters to GROMACS format by Thomas Piggot,
> July 2010.
> ; Also added some parameters from later CHARMM27 versions, such as those
> for the PS headgroup.
> ;
> ; If you use these parameters please check out the forcefield.doc for
> papers to cite
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 1.0 1.0
>
> ;
> ; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and
> CCL) - Thomas Pigot July 2010
> ;
> [ atomtypes ]
> ;name at.num mass charge ptype sigma epsilon
> C 6 12.01100 0.51 A 0.356359487256 0.46024
> CA 6 12.01100 -0.115 A 0.355005321205 0.29288
> CC 6 12.01100 0.62 A 0.356359487256 0.29288
> CD 6 12.01100 0.000 A 0.356359487256 0.29288 ; partial
> charge def not found
> CE1 6 12.01100 0.000 A 0.372395664183 0.284512 ; partial
> charge def not found
> .
> .
> .
> .
> X NN1 CN1A X 9 180.0 10.46 2
> X NN2 CN3B X 9 180.0 4.184 2
> X CN3 CN3C X 9 180.0 0.4184 2
> X NN2 CN3C X 9 180.0 0.4184 2
> X ON4 P3 X 9 0.0 1.2552 3
>
> [ dihedraltypes ]
> ; i j k l func q0 cq
> NN2B CN4 CN5 HN2 2 0.0 58.576
> NN2G CN4 CN1 HN2 2 0.0 6.6944
> NN1 CN2 HN1 HN1 2 0.0 50.208
> CN1 NN2G CN5G ON1 2 0.0 753.12
> CN1T NN2B NN2U ON1 2 0.0 920.48
> CN1 NN2U CN3T ON1 2 0.0 753.12
> CN2 NN3G NN2G NN1 2 0.0 334.72
> CN2 NN3A CN5 NN1 2 0.0 334.72
> CN2 NN3 CN3 NN1 2 0.0 502.08
> CN4 NN2G NN3I HN3 2 0.0 326.352
> CN3 CN3C CN8 HN6 2 0.0 125.52
> HN2 CN3 CN3B NN2 2 0.0 418.4
> HN1 HN1 CN1A NN1 2 0.0 -41.84
> HN8 CN3 CN3 CN8 2 0.0 150.624
> HR1 NR1 NR2 CPH2 2 0.00 4.184
> HR1 NR2 NR1 CPH2 2 0.00 4.184
> HR3 CPH1 NR1 CPH1 2 0.00 4.184
> HR3 CPH1 NR2 CPH1 2 0.00 4.184
> HR3 NR1 CPH1 CPH1 2 0.00 4.184
> HR3 NR2 CPH1 CPH1 2 0.00 4.184
> NR1 CPH1 CPH2 CN7B 2 0.00 5.0208
> NR1 CPH2 CPH1 CN7B 2 0.00 5.0208
> HN2 X X NN2 2 0.0 8.368
> HN1 X X NN1 2 0.0 33.472
> CN1 X X ON1 2 0.0 753.12
> CN1T X X ON1 2 0.0 753.12
> CN1 X X ON1C 2 0.0 669.44
> CN2 X X NN1 2 0.0 753.12
> CN9 X X CN3T 2 0.0 117.152
> HN3B X X CN3 2 0.0 125.52
> HN3B X X CN3A 2 0.0 108.784
> HN3B X X CN3B 2 0.0 108.784
> ON1 X X CN1A 2 0.0 334.72
> HN3 X X CN3C 2 0.0 443.504
> HN6 X X CN3C 2 0.0 443.504
>
>
> ; Include chain topologies
> ;
> ; File 'topol_Protein_chain_A.itp' was generated
> ; By user: shima (1000)
> ; On host: linux-cbyo.site
> ; At date: Wed Dec 12 12:17:55 2012
> ;
> ; This is a include topology file
> ;
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.5.5
> ;
> ; Command line was:
> ; pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p
> ;
> ; Force field was read from current directory or a relative path - path
> added.
> ;
>
> [ moleculetype ]
> ; Name nrexcl
> Protein_chain_A 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> ; residue 1 FVAL rtp FVAL q 0.0
> 1 C 1 FVAL CN 1 0.357 12.011 ;
> qtot 0.357
> 2 HA 1 FVAL H1 2 0.1 1.008 ;
> qtot 0.457
> 3 O 1 FVAL ON 3 -0.51 15.999 ;
> qtot -0.053
> 4 NH1 1 FVAL N 4 -0.423 14.007 ;
> qtot -0.476
> 5 H 1 FVAL HN 5 0.333 1.008 ;
> qtot -0.143
> .
> .
> .
> 359 OC 24 GLY OT1 359 -0.67 15.999 ;
> qtot 1.67
> 360 OC 24 GLY OT2 360 -0.67 15.999 ;
> qtot 1
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 4 1
> .
> .
> .
> .
> 357 360 1
>
> [ angles ]
> ; ai aj ak funct c0 c1
> c2 c3
> 2 1 3 5
> 2 1 4 5
> .
> .
> .
> .
> 355 358 360 5
> 359 358 360 5
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 2 1 4 5 9
> 2 1 4 6 9
> 3 1 4 5 9
> .
> .
> .
> 357 355 358 359 9
> 357 355 358 360 9
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3
> 1 4 3 2 2
> 20 18 22 21 2
> 29 22 31 30 2
> 31 29 33 32 2
> 48 33 50 49 2
> 50 48 52 51 2
> 55 52 57 56 2
> 57 55 59 58 2
> 74 59 76 75 2
> 76 74 78 77 2
> 85 78 87 86 2
> 87 85 89 88 2
> 104 89 106 105 2
> 106 104 108 107 2
> 114 108 116 115 2
> 116 114 118 117 2
> 134 118 136 135 2
> 136 134 138 137 2
> 145 138 147 146 2
> 147 145 149 148 2
> 161 149 163 162 2
> 163 161 165 164 2
> 171 165 173 172 2
> 173 171 175 174 2
> 187 175 189 188 2
> 189 187 191 190 2
> 198 191 200 199 2
> 200 198 202 201 2
> 217 202 219 218 2
> 219 217 221 220 2
> 227 221 229 228 2
> 229 227 231 230 2
> 251 231 253 252 2
> 253 251 255 254 2
> 262 255 264 263 2
> 264 262 266 265 2
> 282 266 284 283 2
> 284 282 286 285 2
> 292 286 294 293 2
> 294 292 296 295 2
> 307 313 310 309 2
> 316 296 318 317 2
> 318 316 320 319 2
> 327 320 329 328 2
> 329 327 331 330 2
> 342 348 345 344 2
> 351 331 353 352 2
> 353 351 355 354 2
> 358 355 360 359 2
>
> [ cmap ]
> ; ai aj ak al am funct
> 18 20 22 29 31 1
> 29 31 33 48 50 1
> 48 50 52 55 57 1
> .
> .
> .
> 292 294 296 316 318 1
> 316 318 320 327 329 1
> 327 329 331 351 353 1
>
> ; Include Position restraint file
> ; In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
>
>
Here's where you start to have problems. This directive was definitely
created by pdb2gmx, which by default restrains only heavy atoms.
> [ position_restraints ]
> ; atom type fx fy fz
> 1 1 1000 1000 1000
> 3 1 1000 1000 1000
> 4 1 1000 1000 1000
> 6 1 1000 1000 1000
>
Now here is another restraint directive that clearly you have created,
which contradicts the directive above. You should only ever have one [
position_restraints ] directive in your topology. I don't know how this
would have arisen, unless you have #included a position restraint file
within the protein chain topology, in which case you're actually #including
two restraint definitions. Don't do that.
> ; position restraints for a_1-360 of Protein
>
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 100000 100000 100000
> 2 1 100000 100000 100000
> 3 1 100000 100000 100000
> 4 1 100000 100000 100000
>
>
<snip>
[ moleculetype ]
> ; Name nrexcl
> Protein_chain_B 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> ; residue 1 FVAL rtp FVAL q 0.0
> 1 C 1 FVAL CN 1 0.357 12.011 ;
> qtot 0.357
> 2 HA 1 FVAL H1 2 0.1 1.008 ;
> qtot 0.457
> 3 O 1 FVAL ON 3 -0.51 15.999 ;
> qtot -0.053
> 4 NH1 1 FVAL N 4 -0.423 14.007 ;
> qtot -0.476
> .
> .
> .
> .
> 359 OC 24 GLY OT1 359 -0.67 15.999 ;
> qtot 1.67
> 360 OC 24 GLY OT2 360 -0.67 15.999 ;
> qtot 1
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 4 1
> 4 5 1
> 4 6 1
> 6 7 1
> .
> .
> .
> .
>
>
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 7 1
> 1 8 1
> 1 18 1
> 2 5 1
> .
> .
> .
>
>
>
> [ angles ]
> ; ai aj ak funct c0 c1
> c2 c3
> 2 1 3 5
> 2 1 4 5
> 3 1 4 5
> 1 4 5 5
> .
> .
> .
> .
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 2 1 4 5 9
> 2 1 4 6 9
> 3 1 4 5 9
> 3 1 4 6 9
> .
> .
> .
>
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3
> 1 4 3 2 2
> 20 18 22 21 2
> 29 22 31 30 2
> 31 29 33 32 2
> .
> .
> .
>
> [ cmap ]
> ; ai aj ak al am funct
> 18 20 22 29 31 1
> 29 31 33 48 50 1
> .
> .
> .
>
>
> ; Include Position restraint file
>
> ; position restraints for a_360-720 of Protein
>
>
Again, this is clearly wrong since you start restraining from atom 360 and
onward, so this must have come from your incorrect usage of genrestr
before. Restraints can't be applied using these atom numbers and should
have triggered a fatal error.
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 360 1 100000 100000 100000
> 361 1 100000 100000 100000
>
>
My suggestion would be to revert to your original topology, do not #include
any custom restraints to your protein, because (1) you almost certainly do
not need them and (2) you have not created them correctly. The only
modification you need to make is with respect to the lipid restraints,
which are #included correctly based on your previous messages.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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