[Chimera-users] residue number in Gromacs tpr file

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 17 15:55:04 PDT 2014

Hi Mario,
	Please try the daily build.  It has code that should assign unique IDs to your chains (though they'll be A-D rather than O/P/g/h) and number each chain starting at one.  I don't think the .tpr file has the info for preserving the original numbering and chain IDs, though I'm not 100% certain without an example multi-chain .tpr file (I only have single-chain files) and using the example .tpr with various Gromacs utilities (e.g. gmxdump).  So if you wanted to send your .tpr file, that would be helpful -- and a couple of frames of your trajectory would be even more helpful though not absolutely necessary.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Mar 15, 2014, at 2:51 AM, Mario Dejung wrote:

> 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
> and
> ; 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
> Mario
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> Chimera-users at cgl.ucsf.edu
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