[gmx-users] coenzyme-protein complex
Justin Lemkul
jalemkul at vt.edu
Wed Jan 8 13:35:03 CET 2014
On 1/8/14, 6:54 AM, Mostafa Javaheri wrote:
> Dear Justin
>
> >The [atomtypes] directive is at the force field level, so any new [atomtypes]
> >need to be declared before any [moleculetypes] appear in the topology. See
> >Chapter 5 for the required hierarchy.
>
> As you consider the [atomtypes] directive in GTP.itp and GDP.itp declared before
> any [moleculetypes], (for shortening they didn't include [ bonds ], [ pairs ], [
> angles ], [ dihedrals ] and [ position_restraints ]); I think this error
> occurres because of the [atomtypes] directive in both GDP.itp and GTP.itp have
> exactly the same prameters, pay attention this only happens when I treat them
> individually (GTP.itp and GDP.itp) and adding both of them (GTP.pdb and GDP.pdb)
> to conf.pdb file but when I treat e.g. only GDP no error will occures, the same
> thing happens for GTP too, also when I treat them as one merged file (GTPGDP.itp
> and GTPGDP.pdb) again no error will appears.
>
I'm not sure I follow this. From what you show below, both molecules introduce
new [atomtypes] and [pairtypes], which are essentially extensions of
ffnonbonded.itp. The problem you have is that each topology attempts to behave
as a standalone topology, which it is not. You will have to manually edit the
topologies, either by:
1. Creating a single file, e.g. "more_parameters.itp" that contains the
necessary [atomtypes] and [pairtypes] that you #include immediately after the
#include "charmm27.ff/forcefield.itp" statement. Remove those directives from
GTP.itp and GDP.itp.
2. Remove the directives from one of the ligand .itp files, and just #include
the other one first, again immediately after #include
"charmm27.ff/forcefield.itp." That way, the first .itp file contains force
field-level directives, after which everything else is at the molecule level,
within the first #included topology and all the remaining ones.
>
> >These notes indicate possible problems with the .mdp file, but since you haven't
> >provided that file, it's impossible to say what may or may not be wrong.
>
> The em.mdp file used for energy minimization provided at the end of this post.
>
> ************************************
> ; ----
> ; Built itp for GTP.mol2
> ; by user vzoete Sat Jan 4 11:31:40 CET 2014
> ; ----
> ;
>
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon
> NC=O 7 14.0067 0.0 A 0.329632 0.836800
> C=O 6 12.0110 0.0 A 0.356359 0.460240
> N=C 7 14.0067 0.0 A 0.329632 0.836800
> C5A 6 12.0110 0.0 A 0.363487 0.209200
> C5B 6 12.0110 0.0 A 0.363487 0.209200
> N5B 7 14.0067 0.0 A 0.329632 0.836800
> NPYL 7 14.0067 0.0 A 0.306469 0.376560
> PO4 15 30.9738 0.0 A 0.383086 2.447640
> HNCO 1 1.0079 0.0 A 0.040001 0.192464
> HOR 1 1.0079 0.0 A 0.040001 0.192464
> HCMM 1 1.0079 0.0 A 0.235197 0.092048
> CR 6 12.0110 0.0 A 0.387541 0.230120
> O2CM 8 15.9994 0.0 A 0.302905 0.502080
> NC=C 7 14.0067 0.0 A 0.329632 0.836800
> OR 8 15.9994 0.0 A 0.315378 0.636386
> O=C 8 15.9994 0.0 A 0.302905 0.502080
>
>
> [ pairtypes ]
> ; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
> CR NC=O 1 0.334087 0.187114
> CR C=O 1 0.347450 0.138768
> CR N=C 1 0.334087 0.187114
> CR C5A 1 0.351014 0.093557
> CR C5B 1 0.351014 0.093557
> CR N5B 1 0.334087 0.187114
> CR NPYL 1 0.322505 0.125520
> CR PO4 1 0.360814 0.320014
> CR HNCO 1 0.189271 0.089737
> CR HOR 1 0.189271 0.089737
> CR HCMM 1 0.286869 0.062059
> CR CR 1 0.338541 0.041840
> CR O2CM 1 0.320723 0.144938
> CR NC=C 1 0.334087 0.187114
> CR OR 1 0.326960 0.163176
> CR O=C 1 0.293997 0.144938
> O=C NC=O 1 0.289542 0.648182
> O=C C=O 1 0.302905 0.480705
> O=C N=C 1 0.289542 0.648182
> O=C C5A 1 0.306469 0.324091
> O=C C5B 1 0.306469 0.324091
> O=C N5B 1 0.289542 0.648182
> O=C NPYL 1 0.277960 0.434814
> O=C PO4 1 0.316269 1.108563
> O=C HNCO 1 0.144726 0.310857
> O=C HOR 1 0.144726 0.310857
> O=C HCMM 1 0.242324 0.214978
> O=C O2CM 1 0.276179 0.502080
> O=C NC=C 1 0.289542 0.648182
> O=C OR 1 0.282415 0.565258
> O=C O=C 1 0.249452 0.502080
>
> [ moleculetype ]
> ; Name nrexcl
> GTP 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 NC=O 1 LIG N1 1 -0.4900 14.0067
> 2 C=O 1 LIG C2 2 0.5600 12.0110
> 3 N=C 1 LIG N3 3 -0.5760 14.0067
> 4 C5A 1 LIG C4 4 -0.0256 12.0110
> 5 C5B 1 LIG C5 5 0.1412 12.0110
> 6 C=O 1 LIG C6 6 0.7160 12.0110
> 7 N5B 1 LIG N7 7 -0.5653 14.0067
> 8 C5A 1 LIG C8 8 0.0365 12.0110
> 9 NPYL 1 LIG N9 9 0.0476 14.0067
> 10 PO4 1 LIG PA 10 1.4424 30.9738
> 11 PO4 1 LIG PB 11 1.4424 30.9738
> 12 PO4 1 LIG PG 12 1.3712 30.9738
> 13 HNCO 1 LIG HN1 13 0.3700 1.0079
> 14 HNCO 1 LIG HN21 14 0.4000 1.0079
> 15 HNCO 1 LIG HN22 15 0.4000 1.0079
> 16 HOR 1 LIG HO2' 16 0.4000 1.0079
> 17 HOR 1 LIG HO3' 17 0.4000 1.0079
> 18 HCMM 1 LIG H1' 18 0.0000 1.0079
> 19 CR 1 LIG C1' 19 0.5356 12.0110
> 20 O2CM 1 LIG O1A 20 -0.9500 15.9994
> 21 O2CM 1 LIG O1B 21 -0.9500 15.9994
> 22 O2CM 1 LIG O1G 22 -1.0333 15.9994
> 23 NC=C 1 LIG N2 23 -0.8500 14.0067
> 24 OR 1 LIG O2' 24 -0.6800 15.9994
> 25 HCMM 1 LIG H2' 25 0.0000 1.0079
> 26 CR 1 LIG C2' 26 0.2800 12.0110
> 27 O2CM 1 LIG O2A 27 -0.9500 15.9994
> 28 O2CM 1 LIG O2B 28 -0.9500 15.9994
> 29 O2CM 1 LIG O2G 29 -1.0333 15.9994
> 30 CR 1 LIG C3' 30 0.2800 12.0110
> 31 OR 1 LIG O3' 31 -0.6800 15.9994
> 32 HCMM 1 LIG H3' 32 0.0000 1.0079
> 33 OR 1 LIG O3A 33 -0.5424 15.9994
> 34 OR 1 LIG O3B 34 -0.5424 15.9994
> 35 O2CM 1 LIG O3G 35 -1.0333 15.9994
> 36 CR 1 LIG C4' 36 0.2800 12.0110
> 37 HCMM 1 LIG H4' 37 0.0000 1.0079
> 38 OR 1 LIG O4' 38 -0.5600 15.9994
> 39 OR 1 LIG O5' 39 -0.5512 15.9994
> 40 CR 1 LIG C5' 40 0.2800 12.0110
> 41 O=C 1 LIG O6 41 -0.5700 15.9994
> 42 HCMM 1 LIG H8 42 0.1500 1.0079
> 43 HCMM 1 LIG HC1 43 0.0000 1.0079
> 44 HCMM 1 LIG HC2 44 -0.0001 1.0079
> ************************************
> GTP.itp
>
> ************************************
> ; ----
> ; Built itp for GDP.mol2
> ; by user vzoete Sun Jan 5 12:52:42 CET 2014
> ; ----
> ;
>
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon
> NC=O 7 14.0067 0.0 A 0.329632 0.836800
> C=O 6 12.0110 0.0 A 0.356359 0.460240
> N=C 7 14.0067 0.0 A 0.329632 0.836800
> C5A 6 12.0110 0.0 A 0.363487 0.209200
> C5B 6 12.0110 0.0 A 0.363487 0.209200
> N5B 7 14.0067 0.0 A 0.329632 0.836800
> NPYL 7 14.0067 0.0 A 0.306469 0.376560
> PO4 15 30.9738 0.0 A 0.383086 2.447640
> HNCO 1 1.0079 0.0 A 0.040001 0.192464
> HOR 1 1.0079 0.0 A 0.040001 0.192464
> HCMM 1 1.0079 0.0 A 0.235197 0.092048
> CR 6 12.0110 0.0 A 0.387541 0.230120
> O2CM 8 15.9994 0.0 A 0.302905 0.502080
> NC=C 7 14.0067 0.0 A 0.329632 0.836800
> OR 8 15.9994 0.0 A 0.315378 0.636386
> O=C 8 15.9994 0.0 A 0.302905 0.502080
>
>
> [ pairtypes ]
> ; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
> CR NC=O 1 0.334087 0.187114
> CR C=O 1 0.347450 0.138768
> CR N=C 1 0.334087 0.187114
> CR C5A 1 0.351014 0.093557
> CR C5B 1 0.351014 0.093557
> CR N5B 1 0.334087 0.187114
> CR NPYL 1 0.322505 0.125520
> CR PO4 1 0.360814 0.320014
> CR HNCO 1 0.189271 0.089737
> CR HOR 1 0.189271 0.089737
> CR HCMM 1 0.286869 0.062059
> CR CR 1 0.338541 0.041840
> CR O2CM 1 0.320723 0.144938
> CR NC=C 1 0.334087 0.187114
> CR OR 1 0.326960 0.163176
> CR O=C 1 0.293997 0.144938
> O=C NC=O 1 0.289542 0.648182
> O=C C=O 1 0.302905 0.480705
> O=C N=C 1 0.289542 0.648182
> O=C C5A 1 0.306469 0.324091
> O=C C5B 1 0.306469 0.324091
> O=C N5B 1 0.289542 0.648182
> O=C NPYL 1 0.277960 0.434814
> O=C PO4 1 0.316269 1.108563
> O=C HNCO 1 0.144726 0.310857
> O=C HOR 1 0.144726 0.310857
> O=C HCMM 1 0.242324 0.214978
> O=C O2CM 1 0.276179 0.502080
> O=C NC=C 1 0.289542 0.648182
> O=C OR 1 0.282415 0.565258
> O=C O=C 1 0.249452 0.502080
>
> [ moleculetype ]
> ; Name nrexcl
> GDP 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 NC=O 1 LIG N1 1 -0.4900 14.0067
> 2 C=O 1 LIG C2 2 0.5600 12.0110
> 3 N=C 1 LIG N3 3 -0.5760 14.0067
> 4 C5A 1 LIG C4 4 -0.0256 12.0110
> 5 C5B 1 LIG C5 5 0.1412 12.0110
> 6 C=O 1 LIG C6 6 0.7160 12.0110
> 7 N5B 1 LIG N7 7 -0.5653 14.0067
> 8 C5A 1 LIG C8 8 0.0365 12.0110
> 9 NPYL 1 LIG N9 9 0.0476 14.0067
> 10 PO4 1 LIG PA 10 1.4424 30.9738
> 11 PO4 1 LIG PB 11 1.3712 30.9738
> 12 HNCO 1 LIG HN1 12 0.3700 1.0079
> 13 HNCO 1 LIG HN21 13 0.4000 1.0079
> 14 HNCO 1 LIG HN22 14 0.4000 1.0079
> 15 HOR 1 LIG HO2' 15 0.4000 1.0079
> 16 HOR 1 LIG HO3' 16 0.4000 1.0079
> 17 HCMM 1 LIG H1' 17 0.0000 1.0079
> 18 CR 1 LIG C1' 18 0.5356 12.0110
> 19 O2CM 1 LIG O1A 19 -0.9500 15.9994
> 20 O2CM 1 LIG O1B 20 -1.0333 15.9994
> 21 NC=C 1 LIG N2 21 -0.8500 14.0067
> 22 HCMM 1 LIG H2' 22 0.0000 1.0079
> 23 OR 1 LIG O2' 23 -0.6800 15.9994
> 24 CR 1 LIG C2' 24 0.2800 12.0110
> 25 O2CM 1 LIG O2A 25 -0.9500 15.9994
> 26 O2CM 1 LIG O2B 26 -1.0333 15.9994
> 27 HCMM 1 LIG H3' 27 0.0000 1.0079
> 28 OR 1 LIG O3' 28 -0.6800 15.9994
> 29 CR 1 LIG C3' 29 0.2800 12.0110
> 30 OR 1 LIG O3A 30 -0.5424 15.9994
> 31 O2CM 1 LIG O3B 31 -1.0333 15.9994
> 32 CR 1 LIG C4' 32 0.2800 12.0110
> 33 HCMM 1 LIG H4' 33 0.0000 1.0079
> 34 OR 1 LIG O4' 34 -0.5600 15.9994
> 35 OR 1 LIG O5' 35 -0.5512 15.9994
> 36 CR 1 LIG C5' 36 0.2800 12.0110
> 37 O=C 1 LIG O6 37 -0.5700 15.9994
> 38 HCMM 1 LIG H8 38 0.1500 1.0079
> 39 HCMM 1 LIG HC1 39 0.0000 1.0079
> 40 HCMM 1 LIG HC2 40 -0.0001 1.0079
> ************************************
> GDP.itp
>
> ************************************
> ; LINES STARTING WITH ';' ARE COMMENTS
> title = Minimization ; Title of run
>
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol
> emstep = 0.01 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to perform
> energygrps = system ; Which energy group(s) to write to disk
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long
> range forces
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
> rlistlong = 1.4
> coulombtype = PME ; Treatment of long range electrostatic interactions
> vdwtype = switch
> rcoulomb = 1.2 ; long range electrostatic cut-off
> rvdw = 1.2 ; long range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
> ************************************
>
These settings all look reasonable, though please be aware we have discovered a
problem that I believe may be important: http://redmine.gromacs.org/issues/1413.
Without a resolution to issue 1413, I cannot necessarily guarantee that
Gromacs and CHARMM treat the cutoffs the same way. We are looking into this.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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