[gmx-users] restraining ligand for position restraint simulation

[Justin A. Lemkul]

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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