<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR>It well done! thank you very much! </DIV>
<DIV>zhao <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7日，周五, 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: "Gromacs Users' List" <gmx-users@gromacs.org><BR>日期: 2010年5月7日,周五,下午10:15<BR><BR>
<DIV class=plainMail><BR>I discovered the problem. There was a case of pattern matching that wasn't working, so an extra bond was being written between atom 0 and atom 0, which of course is nonsense.<BR><BR>Also be advised that the .psf file was mangled anyway, since you had tried to process different topologies (that didn't work), with the end result being concatenation to the .psf file. If you get a non-functional .psf file, delete it, or else top2psf will happily append to your existing .psf file, generating more nonsense.<BR><BR>The end result is that I have fixed the script and uploaded a new version here:<BR><BR><A href="http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD" target=_blank>http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD</A><BR><BR>-Justin<BR><BR>xi zhao wrote:<BR>> <BR>> thank you for your help!<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7日，周五, 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7日,周五,下午7:40<BR>> <BR>> <BR>> <BR>> xi zhao wrote:<BR>> ><BR>> ><BR>> > Yes, the PSF file has NBOND section and the script finished<BR>> without any errors! But it does not show any bonded!<BR>> > Thank you！<BR>> <BR>> Can you send me your coordinate file and .psf file (off-list) so I<BR>> can see if there's anything to diagnose? If you have an NBOND<BR>> section, the script has done its job and should work.<BR>> <BR>> -Justin<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>> ><BR>> > --- *10年5月7日，周五, 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: "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>> <<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7日,周五,下午7:10<BR>> ><BR>> ><BR>> ><BR>> > xi zhao wrote:<BR>> > ><BR>> > > Yes， I load my coarse-grained PDB ,then load ps as data,<BR>> but the<BR>> > stucture still was full of points .<BR>> >
><BR>> ><BR>> > Is a proper "!NBOND" section generated in your .psf file? If the<BR>> > script finishes without any errors, the output should be viable.<BR>> ><BR>> > -Justin<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://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>> > <<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 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 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>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></DIV></BLOCKQUOTE></td></tr></table><br>