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
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--- *12年6月3日，周日, Justin A. Lemkul /<jalem...@vt.edu>/* 写道：
发件人: Justin A. Lemkul <jalem...@vt.edu>
主题: Re: [gmx-users] Atomtype 1
收件人: "Discussion list for GROMACS users" <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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