[gmx-users] DOPC simulation

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Oct 4 20:54:41 CEST 2006

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
Thank you in advance.

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