<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">produce input file , in coarse grained , no standard protein top file <BR><BR><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6日，周四, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> 写道：<BR>
<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: "Gromacs Users' List" <gmx-users@gromacs.org><BR>日期: 2010年5月6日,周四,上午10:37<BR><BR>
<DIV class=plainMail><BR><BR>xi zhao wrote:<BR>> in fact, how to deal with format problem in coarse-grained ?<BR><BR>What do you mean?<BR><BR>-Justin<BR><BR>> thank you!<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>> --- *10年5月6日，周四, Justin A. Lemkul /<<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>>/* 写道：<BR>> <BR>> <BR>> 发件人: Justin A. Lemkul <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>><BR>> 主题: Re:
[gmx-users] how to show structure results in Martini<BR>> coarse-grained simulation?<BR>> 收件人: "Gromacs Users' 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>> 日期: 2010年5月6日,周四,上午9:40<BR>> <BR>> <BR>> <BR>> xi zhao wrote:<BR>> ><BR>> > Dear Sir :<BR>> > The script require what format for top file? my top file is here:<BR>> ><BR>> <BR>> The input is the actual protein topology, not the system topology.<BR>> <BR>> -Justin<BR>> <BR>> > ;<BR>> > ; Example topology file for MARTINI
2.0<BR>> > ;<BR>> > ; First include the file containing all particle definitions,<BR>> > ; the interaction matrix, plus the topology for water.<BR>> > #include "martini_v2.1.itp"<BR>> > #include "martini_v2.0_ions.itp"<BR>> > #include "martini_v2.0_lipids.itp"<BR>> > #include "3ehz.itp"<BR>> > ; Include Position restraint file<BR>> > #ifdef POSRES<BR>> > #include "s.itp"<BR>> > #endif<BR>> > [ system ]<BR>> > CGprotein ion channel<BR>> > [ molecules ]<BR>> > ; name number<BR>> > Protein 1<BR>>
> POPC 502<BR>> > W 18934<BR>> > but run top2psf.pl<BR>> > "Cannot open atoms for reading: No such file or directory"<BR>> > please help me!<BR>> > 4<BR>> <<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>> <<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>> > --- *10年5月3日，周一, Justin A. Lemkul /<<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A><BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu</A>>>/* 写道：<BR>> ><BR>> ><BR>> > 发件人: Justin A. Lemkul <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A><BR>> <<A
href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu</A>>><BR>> > 主题: Re: [gmx-users] how to show structure results in Martini<BR>> > coarse-grained simulation?<BR>> > 收件人: "Discussion list for GROMACS users"<BR>> <<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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org</A>>><BR>> > 日期: 2010年5月3日,周一,上午8:08<BR>>
><BR>> ><BR>> ><BR>> > xi zhao wrote:<BR>> > > Dear user:<BR>> > > how to show struture or conformation in Martini coarse-grained<BR>> > 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<BR>> > 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<BR>> > <<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>> <<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>> > <<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>> <<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>> > 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org</A>><BR>> > <<A
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ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>><BR>> > <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>>.<BR>> > Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=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<BR>> posting!<BR>> Please don't post (un)subscribe requests to the list. Use the www<BR>> interface or send it to <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org"
target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>>.<BR>> Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</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
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