[gmx-users] restraining ligand for position restraint simulation

[Halie Shah]

Hi,

I think this was answered earlier but I didn't quite understand the answer
given.

Hi Hitesh,

The posre.itp file only contains a header [ position_restraints ]
followed by a list of atom numbers and restraint force constants.

Check chapter 5 of the manual for how and what. For a ligand it's
probably best to directly add the [ position_restraints  ] section in
the file with the [ molecule_type ] definition, possibly enclosed by
the statements #ifdef POSRES and #endif. Mind that the aom numbers

need to refer to the atom numbers within the molecule_type definition
and are not related to the atom numbers in the coordinate file.

Cheers,

Tsjerk

On Wed, Apr 15, 2009 at 9:05 AM, Hitesh singla

<hiteshsingla123 at gmail.com
<http://www.gromacs.org/mailman/listinfo/gmx-users>> wrote:
>* Dear all,
*>*
*>* I have generated .itp file for ligand using PRODRG server which i included
*>* in topology file. Now for position restrained dynamics, i wanted to restrain
*>* atom positions for ligand and protein . But porse.itp which generated using
*>* pdb2gmx contain restraints for protein only. Kindly provide me the solution
*>* to restrain ligand atoms.
*>*
*>* Thanks,
*>* Hitesh Singla
*


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:

;       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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