Hello 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 terminus 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 Maria G. Technical University of Denmark Copenhagen
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