<div>Hi Lisa</div>
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<div>Thank you very much for your reply.</div>
<div>After minimimization could I run a molecular dynamic production?</div>
<div>Or have I to do other sets?</div>
<div>Could you write me which are the commands to execute up to MD run?</div>
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<div>Bests<br><br></div>
<div class="gmail_quote">2011/9/22 lina <span dir="ltr"><<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>></span><br>
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<div class="h5">On Thu, Sep 22, 2011 at 11:34 AM, elisa carli <span dir="ltr"><<a href="mailto:elisacarli21@gmail.com" target="_blank">elisacarli21@gmail.com</a>></span> wrote:<br></div></div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear All<br> <br>I'd like to perfom a MD simulation on a membrane protein using DLPC or DPPC system<br>
I've downloaded the API package from this link <a href="http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies" target="_blank">http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies</a><br>
<br>DPPC.zip and DLPC.zip by schiu<br> <br>How can I use them? Where can I get a tutorial or commands illustrating the use of these packages?<br> <br>Thanks in advance <br></blockquote></div></div>
<div> Here is a rough procedure: <br><br><a href="http://www.nanoconductor.org/43A1-S3/" target="_blank">http://www.nanoconductor.org/43A1-S3/</a><br><br>Took Chiu's DPPC.zip as an example. We use the speptide.pdb peptide from the gromacs tutorial (it's a bad choice to put it in the dppc, but we just try it).<br>
<br>pdb2gmx_g -f speptide.pdb -o speptide.gro<br><br>choose <br>9: GROMOS96 43a1 force field<br>1: SPC simple point charge, recommended<br><br>$ tail -1 dppc.gro <br> 5.68585 5.60685 6.85739<br><br>To be as simple as possible here, we use the dimension of the dppc.gro<br>
<br>editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5 4.2 -box 5.68585 5.60685 6.85739<br> <br>now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by<br><br>genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top<br>
<br><br>Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,<br><br>the purpose of doing a simple energy minimization here just want to "test" the topol.top.<br><br>it used 43A1-S3 force field (You can download from <a href="http://www.nanoconductor.org/43A1-S3/" target="_blank">http://www.nanoconductor.org/43A1-S3/</a>).<br>
<br>The head of topol.top: <br>; Include forcefield parameters<br>#include "ffG43A1-S3.itp" <br>#include "lipids_43A1-S3.itp"<br><br>The tail of topol.top:<br><br>[ molecules ]<br>; Compound #mols<br>
Protein 1<br>DPPC 71<br>SOL 3205<br><br>I manually added DPPC 71.<br><br>please copy the lipids_43A1-S3.itp ffG43A1-S3.itp ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into current directory,<br>
extra copy ff_dum.itp from some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current working directory.<br><br>I attached all those files in try.tar.gz<br><a href="https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB" target="_blank">https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB</a><br>
<br>mdrun_g -v -deffnm em<br><br>works well. </div><br clear="all"></div><font color="#888888"><br>-- <br>Best Regards,<br><br>lina<br><br><br></font><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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