<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV> </DIV><DIV>the command "genbox" will automatically take care of overlapping lipids and water molecules with the protein, and make a hole and also insert the protein into the bilayer.. there is no prior requirement of making a hole in the popc bilayer.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Here is quite an in-detail protocol for protein insertion into a bilayer.</DIV><DIV><A href="http://www.dddc.ac.cn/embo04/practicals/9_16.htm">http://www.dddc.ac.cn/embo04/practicals/9_16.htm</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Venky</DIV><DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>Venky Krishnamani</DIV><DIV>Dr.Janos K. Lanyi Lab,</DIV><DIV>D320, Medical Sciences D</DIV><DIV>University of California, Irvine</DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR><DIV><DIV>On May 15, 2006, at 5:13 AM, Shulin Zhuang wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">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"> gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR></BLOCKQUOTE> </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><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. 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