1. Don't use pdb2gmx for lipids. If you want to delete the hydrogens: grep -v " H" dopc.pdb > dopc_noH.pdb then to get a good numbering scheem: editconf -f dopc_noH.pdb -o dopc_noH_renumber.gro (or .pdb)
2. For CHARMM parameters (which I believe Feller uses), there is POPC in top_all27_prot_lipid.rtf. For the united atom alternative, Tieleman's website has popc.itp. In either case, just copy it to a new DOPC definition and modify the palmitoyl into another oleoyl. Alternativey, ask Feller for the parameters.
--Original message-- Hi, all: I'm trying to run a simulation on DOPC bilayer, I've downloaded the pdb file of DOPC from Dr. Scott Feller's website. Currently my questions are: 1. how to delete those hydrogens. When I use pdb2gmx, it complains residue "OLE" not found; 2. how to make the topology file, dopc.itp. I know there's PRODRG, but not sure how to use it properly. It seems that one has to make some modifications to the .itp file produced by it, and I don't know how to do that. Thank you in advance. Jian _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
