[gmx-users] Position restraints

[Mark Abraham]

On 16/06/2011 11:54 AM, Tom Dupree wrote:
> Greetings all,
>
> I have run into a little bit of a problem.
>
> I am trying to simulate a hetro-dimer. Through previous work we have identified 302  C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a significant speed up in simulation time. My supervisor is keen for me to do a comparison of that method with a completely unrestrained system using the 53A6 FF. I managed to generate a position restraint file using the .gro file and genrestr.
> However when I get to the simulation step I can't get grompp to work.

As genrestr -h will warn you, its output is only useful for the first 
molecule.

GROMACS position restraints will not give you any implementation-related 
speed-up, only one from reducing the sampling volume. Freeze groups will 
give you some speed-up (at the cost of making your results depend on 
your frozen configuration), but you will usually not be able to use both 
constraints and NPT as well.

> I ran
>
> genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr

Such a constraint or distance restraint matrix can only work 
intra-[moleculetype], and so is futile for your case.

> As I understand my situation grompp is looking for atom numbers in subset.itp and matching them to the atom numbers in topol_Protein_chain_x.itp and since the atom numbers in subset.itp are based on the em.gro file it fails/goes out of range.

Yep

> Thanks to some chain breaks in my structure I have 6 chains instead of 2, is there a way convert the .gro numbers into the .itp numbers? and hence generate my restraint files based on the topol_Protein_chain_x.itp files?

Sure, use editconf with some appropriate index groups (and maybe -resnr) 
to create subset structures that will then produce output from genrestr 
suitable for use with grompp.

>    Furthermore can I actually do a constraint matrix over multiple molecules?

Not without uniting the [moleculetypes]. Do note that the various kinds 
of restraints, constraints and freeze groups are all distinct 
approaches, and attempting to mix them can be asking for trouble. Be 
sure to use the right terminology when asking for help :-)

Mark

> Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions)
>
>
> All the best,
>
> Tom
>
>
> Fatal error:
> [ file subset.itp, line 145 ]:
> Atom index (5222) in constraints out of bounds (1-5149).
> This probably means that you have inserted topology section "constraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "constraints" section to the right molecule.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> My topology file
> ;
> ;	File 'topol.top' was generated
> ;	By user: onbekend (0)
> ;	On host: onbekend
> ;	At date: Tue May 31 11:44:23 2011
> ;
> ;	This is a standalone topology file
> ;
> ;	It was generated using program:
> ;	pdb2gmx - VERSION 4.5.3
> ;
> ;	Command line was:
> ;	pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v
> ;
> ;	Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_A.itp"
> #endif
> #include "topol_Protein_chain_A2.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_A2.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> #include "topol_Protein_chain_B.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_B.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> #include "topol_Protein_chain_B2.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_B2.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> #include "topol_Protein_chain_B3.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_B3.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> #include "topol_Protein_chain_B4.itp"
> #ifdef POSRES
> #include "posre_Protein_chain_B4.itp"
> #endif
> #ifdef REST
> #include "subset.itp"
> #endif
> ___________________________________________________________________
>
>