[gmx-users] question about gromacs

[Mark Abraham]

Hi,

As genrestr -h warns, you need a position restraint files per moleculetype,
not for the whole set of such molecules.

Mark


On Tue, Feb 4, 2014 at 2:39 PM, Andrew Bostick <andrew.bostick1 at gmail.com>wrote:

> Hi all
>
> My system contain dopc + cholesterol + water + drug molecules.
>
> I want to do MD simulation with position restraint on dopc and cholesterol
> molecules.
>
> I used following lines to obtain posre*.itp files:
>
> genrestr -f npt.gro -n index.ndx -o posre_dopc.itp
>
> genrestr -f npt.gro -n index.ndx -o posre_chol.itp
>
> My topol.top file is as follows:
>
> ; Include forcefield parameters
> #include "gromos-43a1-s3_lipid.ff/forcefield.itp"
>
> #include "cholesterol.itp"
> #ifdef POSRES_chol
> #include "posre_chol.itp"
> #endif
>
> #include "dopc.itp"
> #ifdef POSRES_dopc
> #include "posre_dopc.itp"
> #endif
>
> #include "gromos-43a1-s3_lipid.ff/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 "drug.itp"
>
> [ system ]
> ; Name
> dopc/chol/drug/sol
>
> [ molecules ]
> ; Compound        #mols
> CHOL        26
> DOPC       102
> drg               1
> SOL       4677
>
> When I used grompp, I encountered error:
>
> Fatal error:
> [ file posre_chol.itp, line 34 ]:
> Atom index (30) in position_restraints out of bounds (1-29).
> 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.
>
> I check the GROMACS website at http://www.gromacs.org/Documentation/Errors
> .
> in my opinion my topol.top file is true.
>
> How to fix this error.
>
> Any help will highly appreciated.
> --
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