Check the naming in index file. It might be saying POPC, instead of POP.
On 4/4/07, maite lopez <[EMAIL PROTECTED]> 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
