[Chimera-users] residue number in Gromacs tpr file

Mario Dejung chimera.maillist at dejung.net
Sat Mar 15 02:51:32 PDT 2014

Hi all,
I am experimenting with Gromacs a little bit and try to open the tpr file and the corresponding trajectory in chimera. Works fine, but the numbering is completely wrong. The residues get numbered continuous and not starting at 1 for the next chain.
Not sure if the problem is in the tpr file or in chimera.

I have 4 chains in my pdb file and all have a chain identifier, O P g and h and they are separated by TER
I have also 4 .itp files with names like “topol_Protein_chain_O.itp”
My topol.top file say 4 molecules
[ molecules ]
; Compound        #mols
Protein_chain_O     1
Protein_chain_P     1
Protein_chain_g     1
Protein_chain_h     1

; Include chain topologies
#include "topol_Protein_chain_O.itp"
#include "topol_Protein_chain_P.itp"
#include "topol_Protein_chain_g.itp"
#include “topol_Protein_chain_h.itp"

I create my tpr file with grompp 

Has anybody experience with this kind of issue?

Kind regards
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