[gmx-users] protein membrane simulation

[Viswanadham Sridhara]

Check the naming in index file.
It might be saying POPC, instead of POP.

On 4/4/07, maite lopez <lopezmai at gmail.com> wrote:
> Hi all:
>
> I´m working on membrane peptides simulation under lipid (POPC, from
> Peter Tieleman group site). I downloaded the popc.pdb and lipid.itp
> file from this site and i want to use the ffG53a5 force field. Some
> days ago suggest to me i should to do something like this :
>
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023640.html
>
> These are the steps i followed:
>
> 1. Added [atomtypes] from lipid.itp to ffG53a5nb.itp and to ffG53a5.atp
>
> 2. Added [pairtypes] from lipid.itp to  ffG53a5nb.itp and  removed any
> with reference to HW as it will be zero regardless.
>
> 3. Added [dihedraltypes] from lipid.itp to ffG53a5bon.itp.
>
> My popc128.top file is:
>
> ; Include forcefield parameters
> #include \"ffG53a5.itp\"
>
> ; 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
>
> [ system ]
> ; name
> POPC128 + 2460 water
>
> [ molecules ]
> ; name  number
> POP     128
> SOL     2460
>
> But when i run grompp it gives :
> Fatal error:
> No such moleculetype POP
>
> Could you help me?
>
> another question:
> Have somebody a script for deleting the  water molecules between the
> monolayers (this molecules are added with genbox command).
>
> All comments are very appreciated.
> thanks
> Maite
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-- 
Viswanadham Sridhara,
Research Assistant,
Old Dominion University,
Norfolk, Va-23529.