[gmx-users] protein membrane simulation
muta.mestri at gmail.com
Wed Apr 4 22:12:43 CEST 2007
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 :
> 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
> [ 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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Old Dominion University,
More information about the gromacs.org_gmx-users