Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@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, <scapr...@uniroma3.it<mailto:scapr...@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 -- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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