[gmx-users] Atomtype 1

xi zhao zhaoxiitc2002 at yahoo.com.cn
Sun Jun 3 15:03:37 CEST 2012

in fact, the pdb2gmx still hang. I modified the atomtypes.atp , 
aminoacids.rtp , ffbonded.itp, ffnonbonded.itp , 
aminoacids.hdb, residuetypes.dat
,morever, now the pdb2gmx_d even does not the standard protein structure. 

--- 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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