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Hi,<br>
<br>
It's just hard to know your problem with this information. Can you tell
us what grompp gives for the number of atoms in the .top file and in
the .pdb file?<br>
<br>
<div class="moz-signature"><i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
</div>
<br>
<br>
naga raju wrote:
<blockquote
cite="mid20050831141642.53491.qmail@web8503.mail.in.yahoo.com"
type="cite">
<pre wrap="">Dear gmx-users,
I am getting problem to create
*.tpr file for system containing membrane protein
embeded in lipid bilayer. Here I am giving what i have
done. I took only transmembrane part and deleted
remaining residues in the protein. Missing heavy
atoms are added using SwissPDB Viewer. In this case i
have 10 different helices, each helix saved as
seperate pdb file. To this pdb files i created
topology files using ffgmx force field by pdb2gmx
command.
I renamed *.top as *.itp and then deleted the sentence
after the line "; Include Position restraint file "
for itp file. The generated pdb files (10 different
pdb files) are merged into a single pdb file. I made a
SINGLE.top file using these *.itp files (10 different
itp files). I am getting the following error.
" The number of atoms in coordinate file are not
equal to atoms in topology file." I checked each
individual pdb files and itp files, these have same
number of atoms. Would you tell me how to solve this
problem.(Here I did't take lipid bilayer)
Here is the my SINGLE.top file.
;Topology files generated using ffgmx force field
#include "ffgmx.itp"
#include "h1.itp"
#include "h2.itp"
#include "h3.itp"
#include "h4.itp"
#include "h5.itp"
#include "h6.itp"
#include "h7.itp"
#include "h8.itp"
#include "h9.itp"
#include "h10.itp"
[ system ]
; name
Protein
[ molecules ]
; name number
Protein 10
Thank you
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</pre>
</blockquote>
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