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 <[email protected]>
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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