[gmx-users] Strangeness in gro file

Sweta Iyer iyer at wehi.EDU.AU
Tue Sep 13 07:27:43 CEST 2011

Hi all,
I am trying to use the g_membed tool to insert my protein into a DMPC membrane. 
My protein is a dimer and hence I separated the two monomers by a TER card in the original pdb file before pdb2gmx step for gromacs to identify it as teo separate entities.. I then merged my protein file with that of the membrane and added water and ions to it. Then when I went ahead to make an index file I notice that the numbering of residues is not continuous in my gro file, ie, it starts from residue 1-29 of a monomer, then again 1-29 of the second monomer, 1-128 for the DMPC moleculaes and similarly for the SOL and ions as well. As a result, I cannot exactly specify residue number for my index file to specify the two protein groups as different as the residue numbers overlap. Even when i try to do it, i get an error message saying Atom 1 in multiple T-Coupling groups  Is there a way to re number them so that there is continuity or is there another way around to making the index file? I have not seen this the previously when I have made an index file. I am using gmx version 4.5.4 and the 53a6 forcefield. I am not attaching the gro file here as it is quite lengthy.
Thank you for your time.

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