Hello gmx users,
when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file.
Could something be wrong with the pdb2gmx program?
Thank you in advance for any suggestions.
Sincerely,
Michael Owen
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