[gmx-users] Atomtype 1

[Justin A. Lemkul]

On 6/3/12 9:37 AM, xi zhao wrote:
>
> in windows , I use ultraedit, in linux ,use vi

Does pdb2gmx crash in both cases?

If it does, we'll need more information, including what exactly you've done to 
each file (i.e. show the contents) because there's an outside chance something 
else may be going wrong.  Also, knowing your Gromacs version would be useful as 
well.  I seem to remember a relevant bug a while back that was fixed long ago, 
so if you're not using 4.5.5, please upgrade and try again.

-Justin

>
> 4
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> --- *12年6月3日，周日, Justin A. Lemkul /<jalemkul at vt.edu>/* 写道：
>
>
>     发件人: Justin A. Lemkul <jalemkul at vt.edu>
>     主题: Re: [gmx-users] Atomtype 1
>     收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     日期: 2012年6月3日,周日,下午9:19
>
>
>
>     On 6/3/12 9:16 AM, xi zhao wrote:
>      >
>      > I use Ultraedit to produce new part and paste the files; we add a residue
>     name
>      > and corresponding atom type and interaction parameters
>      >
>
>     Having never used a commercial text editor, I don't know if its integrity. What
>     happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad
>     (Windows)? What operating system are you using?
>
>     The only times I've had pdb2gmx die when reading atom types are when the line
>     endings are bad, so I would strongly suspect this is your issue.
>
>     -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>>
>      >
>      > --- *12年6月3日，周日, 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] Atomtype 1
>      > 收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      > 日期: 2012年6月3日,周日,下午8:46
>      >
>      >
>      >
>      > On 6/3/12 8:24 AM, xi zhao wrote:
>      > > Dear gmx-users:
>      > > I add a new residue in *rtp ,according to
>      > >
>      >
>     http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
>      > > and modified corresponding files :such as atp, hdb , after making a full
>      > copy of
>      > > the installed forcefield in woring diectory.
>      > > When pdb2gmx_d
>      > > appeared "
>      > > All occupancies are one
>      > > Opening force field file ./amber99sbr.ff/atomtypes.atp
>      > > Atomtype 1"
>      > > Please give me suggestions
>      >
>      > Did the program hang here? Did it crash? What modifications did you make,
>      > and to what files? Are you using a plain text editor that properly treats
>      > newlines?
>      >
>      > -Justin
>      >
>      > -- ========================================
>      >
>      > Justin A. Lemkul, Ph.D.
>      > Research Scientist
>      > 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.
>     Research Scientist
>     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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================