GROMACS

This problem is related to issue #544, in which "pdb2gmx -chainsep interactive" did not work as expected. In version 4.5.4 (and the latest release-4-5-patches), the "-chainsep interactive" option works correctly, but in the case where "-chainsep ter" would also work, pdb2gmx fails. Attached is a .pdb file for which this is the case. There are two chains, A and B, with no TER delimiter between the chains, but there is one at the end. The intent is to obtain a merged moleculetype with chains A and B such that disulfides can be formed between the chains. In the absence of a TER delimiter, the two chains should be merged, but instead ASN 21 is not identified as a terminal residue and thus a fatal error arises that atom OXT cannot be found in (non-terminal) ASN.