<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR>Dear Sir :</DIV>
<DIV>The script require what format for top file? my top file is here: </DIV>
<DIV><BR>;<BR>; Example topology file for MARTINI 2.0<BR>;</DIV>
<DIV>; First include the file containing all particle definitions,<BR>; the interaction matrix, plus the topology for water.</DIV>
<DIV>#include "martini_v2.1.itp"<BR>#include "martini_v2.0_ions.itp"<BR>#include "martini_v2.0_lipids.itp"<BR>#include "3ehz.itp"</DIV>
<DIV>; Include Position restraint file<BR>#ifdef POSRES<BR>#include "s.itp"<BR>#endif</DIV>
<DIV>[ system ]<BR>CGprotein ion channel</DIV>
<DIV>[ molecules ]<BR>; name number<BR>Protein 1<BR>POPC 502<BR>W 18934</DIV>
<DIV>but run top2psf.pl </DIV>
<DIV>"Cannot open atoms for reading: No such file or directory"</DIV>
<DIV>please help me!<BR><A class=plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A><BR><BR>--- <B>10年5月3日，周一, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> 写道：<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>发件人: Justin A. Lemkul <jalemkul@vt.edu><BR>主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?<BR>收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>日期: 2010年5月3日,周一,上午8:08<BR><BR>
<DIV class=plainMail><BR><BR>xi zhao wrote:<BR>> Dear user:<BR>> how to show struture or conformation in Martini coarse-grained simulation, using VMD or other?<BR>> Please give me some suggestion!<BR>> thank you!<BR><BR>What kind of rendering do you want to do? There are some scripts linked below to render bonds in a CG structure.<BR><BR><A href="http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD#VMD_and_coarse-grained_simulations" target=_blank>http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD#VMD_and_coarse-grained_simulations</A><BR><BR>-Justin<BR><BR>> <BR>> <BR>> 4 <<A href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" target=_blank>http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844</A>><BR>> <BR>> <BR>> <BR><BR>--
========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the www interface or
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