[gmx-users] simulation of protein in popc box

Justin A. Lemkul jalemkul at vt.edu
Fri May 22 13:31:39 CEST 2009

Samik Bhattacharya 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.

I would first recommend some tutorial material on simple systems of proteins in 
water before tackling a membrane protein, which is considerably more complicated.

Then, I will suggest you try the following tutorial:



> thank you
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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