I am very new to membrane modeling and hope to see more up-to-date protocols. Wish anyone can share it with us.<br><br>
<div><span class="gmail_quote">On 5/15/06, <b class="gmail_sendername">Graham Smith</b> <<a href="mailto:graham.smith@biiuk.com">graham.smith@biiuk.com</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>> Message: 2<br>> Date: Mon, 15 May 2006 02:32:06 -0700 (PDT)<br>> From: mahbubeh zarrabi <
<a href="mailto:zarrab_m@yahoo.com">zarrab_m@yahoo.com</a>><br>> Subject: [gmx-users] protein in popc<br>> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Message-ID: <<a href="mailto:20060515093206.21682.qmail@web51605.mail.yahoo.com">
20060515093206.21682.qmail@web51605.mail.yahoo.com</a>><br>> Content-Type: text/plain; charset=iso-8859-1<br>><br>> dear freinds<br>> I have made a hole in POPC128a bilayer.But I failed<br>> inputing protein into
it.I run below commands but<br>> there is not protein in the hole.whould you please<br>> help me? do you have another<br>> protocol for protein insertion in popc (in detail)?<br>><br>> make_hole.pl -f popc.pdb
-o popcout.pdb -r 1.4 -lipat<br>> P8 -lipid POP -cx 2.3 -cy 2.8<br>> grompp -f run.mdp -o insert.tpr -c popcout.pdb -p<br>> popc.top<br>> mdrun -v -hole -holep hp.mdp -deffnm insert<br>> -----------------------------------------------------
<br><br>Dear Mahbubeh,<br><br>I don't know if more up-to-date protocols have since been developed, I<br>don't work on membrane proteins any more. However, if you still want to<br>try to use the older hole-making code:<br>
Checks:<br>(a) you are using a special version of mdrun compiled from old gromacs<br>version 3.1.4 and the extra code available from the contributions section<br>(b) you have looked at the html-format tutorial notes.<br>(c) "Hole-making" forces are being generated and applied to certain
<br>atoms: to see this, run with<br>debugsurf = yes<br>in the hp.mdp files and it will stop at step 0 after producing extra<br>pdbs with the dummy atoms to show the forces (see tutorial)<br>(d), Finally, the output of mdrun -v -hole -holep
hp.mdp... will not<br>have the protein inserted directly, but will just have a hole in the<br>right place for your protein to be put in (by combining the pdb or gro<br>files with an editor).<br><br>Graham<br>--<br>Dr Graham R. Smith
<br>Head of Protein-Protein Interactions<br>Biosystems Informatics Institute<br>Newcastle upon Tyne<br>NE1 4EP<br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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</div><br><br clear="all"><br>-- <br> Shulin Zhuang<br>Chemistry Department <br>Zhejiang University PRC<br><a href="mailto:shulin.zhuang@gmail.com">shulin.zhuang@gmail.com</a>