thanks for reply.I want to perform simulation of popc membrane. Steps which i have done are as follows: 1. download popc128a.pdb, popc.it,lipids.itp (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) 2. download ffgmx_lipids files 3.convert POPC of .top & popc.itp into POP as in popc.gro 4. #include "ffgmx.itp" #include "lipid.itp" #include "popc.itp" #include "ffgmxnb.itp" #include "ffgmxbon.itp"
These last two lines should already be included in ffgmx.itp, and including them twice may cause some headaches.
I think that the real problem here is exactly as described in the error message. There is no POP residue in ffgmx.rtp
................ in my .top file. Now when I perform pdb2gmx -ff gmx -f popc128a.pdb -o popc.gro -p popc.top it shows the error that"Residue 'POP' not found in residue topology database". I think that's because of the fact that ffgmx.rtp do not contain "POP" residue ,but it has DPPC residue. Plz suggest how can i solve this problem. thanks.
Use editconf to convert between .pdb and .gro. You only need pdb2gmx if you don't have a .top file, but Prof. Tieleman has kindly provided this for you already, in the form of lipid.itp and popc.itp.
Agreed. There is no need to use pdb2gmx here since you have a popc.itp file already. You need to make your own .top file. That shouldn't be too difficult. Just look at one you get from pdb2gmx for a protein, make the necessary changes, including lipid.itp and putting POP 128 in the molecules section at the end (or is it POPC not POP for the molecule name? Look at the top of the popc.itp file to see what the name of the molecule is.
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