[gmx-users] Problem in creating *.tpr file

naga raju nagaraju_cy at yahoo.co.in
Wed Aug 31 16:16:41 CEST 2005

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
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

[ molecules ]
; name	number
Protein  10  

               Thank you

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