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
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<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
>
> ========================================
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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
========================================
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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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