[gmx-users] pdb2gmx error after switching force fields

Irem Altan irem.altan at duke.edu
Fri May 13 16:49:19 CEST 2016


I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning:

WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be

The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 85, 95). The weird thing is, the residue numbers in the pdb file start from 107, and gmx complains about lower numbers. Also, have I understood correctly that gmx complains that glycines in my input file don’t have beta carbons? What could be the problem here?


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