[gmx-users] membrane simulation

scaprari at uniroma3.it scaprari at uniroma3.it
Thu May 3 13:08:41 CEST 2012

Hi all,
I'm new in Membrane simulations with Gromacs. I have to simulate a system
made up of a protein just leant on a membrane patch which has previously
been extended and made it free of periodicity (with trjconv). I'm reading
the "KALP15 in DPPCI" Tutorial and, so far, I managed to obtain my protein
(in pdb code) very close to the membrane surface by using editconf and cat
command. At this point, I don't know how to get on. 1)How should I
generate the topology file which includes  the coordinates both of the
protein and of the membrane?
2)Furthermore, the lipid molecules are listed in my pdb file  with the
abbreviation "DPP", whereas I see that those ones are called "DPPC" in the
Tutorial. Therefore, Should I replace "DPP" abbreviation with "DPPC" in my
pdb file? Could this difference cause any bugs in the next steps?
Any suggestion would be appreciated,


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