[gmx-users] unknown residue (BGC)

delara aghaie d_aghaie at yahoo.com
Wed Jun 13 12:32:31 CEST 2012

Dear Gromacs users
I want to create from 1AU1.pdb, the  .gro and .top files.

Running this command

pdb2gmx -ignh -f 1AU1.pdb -o 1AU1.gro -p topo.top -water spce

and choose this forcefield: 

 GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

I get this error:
Fatal error:
Residue 'BGC' not found in residue topology database

How can i fix it?

Also what this message by pdb2gmx means?
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

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