[gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ?

maria goranovic mariagoranovic at gmail.com
Wed Mar 16 11:29:40 CET 2011


I am trying to pdb2gmx with a free amino acid in amber99sb as follows:

pdb2gmx -f temp.pdb -ff amber99sb

there are no ter records in the input pdb file.

However, pdb2gmx fails with the following error:

Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2gmx.c, line: 284

Fatal error:
In the chosen force field there is no residue type for 'GLU' as a starting
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Is this some kind of bug. If so, is there a workaround? For example, can I
have the amino acid bound to the terminus of the larger protein (for which
the free amino acid is a ligand) and make the bond have a zero spring
constant or something?


Maria G.
Technical University of Denmark
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