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On 3/06/2012 11:03 PM, xi zhao wrote:
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<div>in fact, the pdb2gmx still hang. I modified the
atomtypes.atp , <br>
aminoacids.rtp , ffbonded.itp, ffnonbonded.itp , <br>
aminoacids.hdb, residuetypes.dat<img
moz-do-not-send="true" class="pimg" alt="4"
src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"
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,morever, now the pdb2gmx_d even does not the standard
protein structure. </div>
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<br>
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).<br>
<br>
Also, you need to answer the last question Justin asked, because
that answer is likely to reveal your problem...<br>
<br>
Mark<br>
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<div><br>
--- <b>12年6月3日，周日, Justin A. Lemkul <i><a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a></i></b>
写道：<br>
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发件人: Justin A. Lemkul <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a><br>
主题: Re: [gmx-users] Atomtype 1<br>
收件人: "Discussion list for GROMACS users"
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
日期: 2012年6月3日,周日,下午8:46<br>
<br>
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On 6/3/12 8:24 AM, xi zhao wrote:<br>
> Dear gmx-users:<br>
> I add a new residue in *rtp ,according to<br>
> <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>,<br>
> and modified corresponding files :such as atp,
hdb , after making a full copy of<br>
> the installed forcefield in woring diectory.<br>
> When pdb2gmx_d<br>
> appeared "<br>
> All occupancies are one<br>
> Opening force field file
./amber99sbr.ff/atomtypes.atp<br>
> Atomtype 1"<br>
> Please give me suggestions<br>
<br>
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?<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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