[gmx-users] Problem in creating *.tpr file
nagaraju_cy at yahoo.co.in
Wed Aug 31 16:16:41 CEST 2005
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
[ system ]
[ molecules ]
; name number
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