[gmx-users] simulation of protein in popc box

[Samik Bhattacharya]

Thanks pawan, for helping.... but one problem still remains that is how to incorporate the .itp file inside the topology file???? and which .itp file should i include is it the lipid.itp orr POPC.itp??
thanx for your help
Shamik





Greetings from Pawan.
Topologies for lipids like POP are not available in the topology database in gromacs.
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.


Regards,
Pawan

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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