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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
