[gmx-users] how to show structure results in Martini coarse-grained simulation?
xi zhao
zhaoxiitc2002 at yahoo.com.cn
Fri May 7 16:49:36 CEST 2010
It well done! thank you very much!
zhao
--- 10年5月7日，周五, Justin A. Lemkul <jalemkul at vt.edu> 写道：
发件人: Justin A. Lemkul <jalemkul at 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 at 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 /<jalemkul at vt.edu>/* 写道：
>
>
> 发件人: Justin A. Lemkul <jalemkul at 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 at 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 /<jalemkul at vt.edu
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/* 写道：
> >
> >
> > 发件人: Justin A. Lemkul <jalemkul at vt.edu
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@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 at gromacs.org
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@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
> >
> > ========================================
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> >
> -- ========================================
>
> 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 at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before
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> 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
========================================
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