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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>Im Auftrag von </b>Anirban Ghosh<br>
<b>Gesendet:</b> Donnerstag, 3. Mai 2012 13:39<br>
<b>An:</b> Discussion list for GROMACS users<br>
<b>Betreff:</b> Re: [gmx-users] membrane simulation<o:p></o:p></span></p>
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<p class="MsoNormal">On Thu, May 3, 2012 at 4:38 PM, <<a href="mailto:scaprari@uniroma3.it" target="_blank">scaprari@uniroma3.it</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">Hi all,<br>
I'm new in Membrane simulations with Gromacs. I have to simulate a system<br>
made up of a protein just leant on a membrane patch which has previously<br>
been extended and made it free of periodicity (with trjconv). I'm reading<br>
the "KALP15 in DPPCI" Tutorial and, so far, I managed to obtain my protein<br>
(in pdb code) very close to the membrane surface by using editconf and cat<br>
command. At this point, I don't know how to get on. 1)How should I<br>
generate the topology file which includes the coordinates both of the<br>
protein and of the membrane?<o:p></o:p></p>
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<p class="MsoNormal">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 <a href="https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial">https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial</a> . <o:p></o:p></p>
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<p class="MsoNormal">2)Furthermore, the lipid molecules are listed in my pdb file with the<br>
abbreviation "DPP", whereas I see that those ones are called "DPPC" in the<br>
Tutorial. Therefore, Should I replace "DPP" abbreviation with "DPPC" in my<br>
pdb file? Could this difference cause any bugs in the next steps?<o:p></o:p></p>
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<p class="MsoNormal">PDB files use three letter convention for residue names. I think you can change them without any issue in the .gro file.<o:p></o:p></p>
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<p class="MsoNormal">-Anirban<o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">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 *<b>NOT</b>*look
like this<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">ATOM 1 C1 DPP 1 17.610 52.750 30.500 1.00 0.00
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">ATOM 2 C2 DPPC 1 16.160 50.940 30.040 1.00 0.00
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">ATOM 3 C3 DPPC 1 18.640 50.520 29.970 1.00 0.00
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">ATOM 4 N4 DPP 1 17.520 51.490 29.680 1.00 0.00
<o:p></o:p></span></p>
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<p class="MsoNormal">Any suggestion would be appreciated,<br>
<br>
Silvia<br>
<span style="color:#888888"><br>
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