[gmx-users] simulation of protein in popc box

Pawan Kumar pawan.chinari at gmail.com
Fri May 22 13:17:57 CEST 2009


Greetings from Pawan.
Topologies for lipids like POP are not available in the topology database in
So the starting point would be to generate a topology and a gro file for the
protein alone as such and then edit the topology to include the .itp files
as specifically needed for the lipids.


On Fri, May 22, 2009 at 4:42 PM, Samik Bhattacharya
<samikbhat at yahoo.co.in>wrote:

> hi
> i am new to Gromacs. i want to simulate a protein inside a lipid
> box(preferably POPC or POPE). i have generated the protein inside the POPC
> box complex. But whenever i am going to build the .gro and .top file of that
> complex with pdb2gmx an error is creeping in saying "Cant find POP in
> residue topology database". it cant recognise the lipid.itp and popc.itp
> files which i've already put into the top directory.
> plese help me out.
> thank you
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