[gmx-users] Atomtype 1

[xi zhao]

in windows , I use ultraedit, in linux ,use vi 



--- 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>
>
> --- *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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