[gmx-users] simulation of protein in popc box

[Pawan Kumar]

Hello Shamik,

Going through the membrane protein tutorial will help you to get answers to
these questions.
The lipid.itp file has to be modified and edited depending on the force
fields being used like opls force field or the gromos96 force field.
Popc.itp file should also be included in order to include the topology for
the POP residues. lipid.itp file is used to include more of interaction
parameters.

Regards,
Pawan

On Fri, May 22, 2009 at 4:58 PM, Samik Bhattacharya
<samikbhat at yahoo.co.in>wrote:

> 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<http://mc/compose?to=samikbhat@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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