AW: [gmx-users] membrane simulation

[Rausch, Felix]

Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im Auftrag von Anirban Ghosh
Gesendet: Donnerstag, 3. Mai 2012 13:39
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] membrane simulation


On Thu, May 3, 2012 at 4:38 PM, <scaprari at uniroma3.it<mailto:scaprari at uniroma3.it>> wrote:
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?

If you are using the ff53a6 FF then you need to add the appropriate lipid parameters in the ffnonbonded.itp and ffbonded.itp files (of ff53a6 FF) files which is very well explained in the tutorial. Then in your .top file you need to include the DPPC.itp. However, if you are using CHARMM36 FF, then you can directly use pdb2gmx on your system (I suppose DPPC is already included in it). If you wish to use the ff43a1 FF, then you can find the modified .itp files at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial .

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?

PDB files use three letter convention for residue names. I think you can change them without any issue in the .gro file.

-Anirban


You can also simply replace DPP by DPPC in the pdb. But be careful that there is no shifting of the columns after the residue name, i.e. it should *NOT*look like this

ATOM      1  C1  DPP     1      17.610  52.750  30.500  1.00  0.00
ATOM      2  C2  DPPC     1      16.160  50.940  30.040  1.00  0.00
ATOM      3  C3  DPPC     1      18.640  50.520  29.970  1.00  0.00
ATOM      4  N4  DPP     1      17.520  51.490  29.680  1.00  0.00


Any suggestion would be appreciated,

Silvia

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