Halie Shah wrote:

I am trying to do what Hitesh tried to do..get a pos restraint on both my protein and ligand....I found that -DPOSRES only takes into account 1 posre.itp file...so I appended the atom numbers of my ligand (2519-2531) to the end of the posre file for my protein (1-2518). Then I tried running grompp on this and it gave me the error

-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: ../../../src/kernel/toppush.c, line: 1193

Fatal error:
[ file "posre.itp", line 2015 ]:
Atom index (2519) in position_restraints out of bounds (1-2518).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
-------------------------------------------------------

Also, fyi, earlier for energy minimization, I had included the ff for the itp file in [forcefield] section and included HSL (my ligand) in the [molecule] section after putting the coords for the HSL into my protein pdb file. See parts of the top file below:


Position restraints sections must be placed within the same [ moleculetype ] definition. So, you can't include all of the position restraint information in one file, since that file is part of the Protein [ moleculetype ] definition. The ligand should be placed in its own posre.itp file and included in the topology.

These lines must be placed *outside* of the [ moleculetype ] directive of any other molecule(s) in the system. For consistency, whenever I have ligands, I place them immediately after the protein [ moleculetype ] and water topology, i.e.:

#ifdef POSRES
#include "posre.itp"
#endif

#include "ligand.itp"

#ifdef POSRES_LIGAND
#include "ligand_posre.itp"
#endif

#include "spc.itp"

(etc).

That way, the protein [ moleculetype ] ends with the #ifdef POSRES, the ligand section begins with #include "ligand.itp", ends with the POSRES_LIGAND section, and then the topology reads the water topology, etc.

-Justin

P.S. ffgmx is deprecated; you should probably be using a more modern Gromos96 variant. Topologies compatible with ffG43a1 can be produced from the PRODRG beta server. These can also be modified to correspond with newer (i.e, ffG53a6) force fields.

;       File 'BR6.top' was generated
;       By user: onbekend (0)
;       On host: onbekend
;       At date: Wed Apr 29 11:35:48 2009
;
;       This is your topology file
;       "I'll Match Your DNA" (Red Hot Chili Peppers)
;
; Include forcefield parameters
#include "ffgmx.itp"
#include "C4AHLdbMarc.itp"

[ moleculetype ]
; Name            nrexcl
Protein_A           3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1 MET N 1 0.129 14.0067 ; qtot 0.129 2 H 1 MET H1 1 0.248 1.008 ; qtot 0.377 3 H 1 MET H2 1 0.248 1.008 ; qtot 0.625 4 H 1 MET H3 1 0.248 1.008 ; qtot 0.873 5 CH1 1 MET CA 1 0.127 13.019 ; qtot 1 6 CH2 1 MET CB 2 0 14.027 ; qtot 1 7 CH2 1 MET CG 3 0 14.027 ; qtot 1 8 S
;etc....end of file below

2509  2507  2514  2510     2
2509  2512  2511  2510     2
2509  2516  2515  2514     2

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
HSL                 1
SOL                 1
SOL             12480
Na                 11


So, is it not possible in GROMACS to restrain multiple molecules together? If it is, how do you do this?

Thanks in advance,
Halie Shah
U of H Briggs Lab


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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
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