It well done! thank you very much! zhao
--- 10年5月7日，周五, Justin A. Lemkul <jalem...@vt.edu> 写道： 发件人: Justin A. Lemkul <jalem...@vt.edu> 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Gromacs Users' List" <gmx-users@gromacs.org> 日期: 2010年5月7日,周五,下午10:15 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. 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. The end result is that I have fixed the script and uploaded a new version here: http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD -Justin xi zhao wrote: > > thank you for your help! > > 4 > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844> > > --- *10年5月7日，周五, Justin A. Lemkul /<jalem...@vt.edu>/* 写道： > > > 发件人: Justin A. Lemkul <jalem...@vt.edu> > 主题: Re: [gmx-users] how to show structure results in Martini > coarse-grained simulation? > 收件人: "Gromacs Users' List" <gmx-users@gromacs.org> > 日期: 2010年5月7日,周五,下午7:40 > > > > xi zhao wrote: > > > > > > Yes, the PSF file has NBOND section and the script finished > without any errors! But it does not show any bonded! > > Thank you！ > > Can you send me your coordinate file and .psf file (off-list) so I > can see if there's anything to diagnose? If you have an NBOND > section, the script has done its job and should work. > > -Justin > > > 4 > ><http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844 > ><http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>> > > > > --- *10年5月7日，周五, Justin A. Lemkul /<jalem...@vt.edu > <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* 写道： > > > > > > 发件人: Justin A. Lemkul <jalem...@vt.edu > <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>> > > 主题: Re: [gmx-users] how to show structure results in Martini > > coarse-grained simulation? > > 收件人: "Gromacs Users' List" <gmx-users@gromacs.org > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>> > > 日期: 2010年5月7日,周五,下午7:10 > > > > > > > > xi zhao wrote: > > > > > > Yes， I load my coarse-grained PDB ,then load ps as data, > but the > > stucture still was full of points . > > > > > > > Is a proper "!NBOND" section generated in your .psf file? If the > > script finishes without any errors, the output should be viable. > > > > -Justin > > > > -- ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- gmx-users mailing list gmx-users@gromacs.org > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org> > > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org> > > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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