On 3/06/2012 11:03 PM, xi zhao wrote:
in fact, the pdb2gmx still hang. I modified the atomtypes.atp ,
aminoacids.rtp , ffbonded.itp, ffnonbonded.itp ,
aminoacids.hdb, residuetypes.dat4
,morever, now the pdb2gmx_d even does not the standard protein structure.
So clearly you have broken the file format, probably of at least
atomtypes.atp. However we can't guess how if we can't see your changes
(e.g. use the diff tool).
Also, you need to answer the last question Justin asked, because that
answer is likely to reveal your problem...
Mark
--- *12?6?3?,??, Justin A. Lemkul /<jalem...@vt.edu>/* ??:
???: Justin A. Lemkul <jalem...@vt.edu>
??: Re: [gmx-users] Atomtype 1
???: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
??: 2012?6?3?,??,??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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