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Bug #784

pdb2gmx -chainsep does not behave as expected

Added by Justin Lemkul about 8 years ago. Updated about 8 years ago.

Status:
Closed
Priority:
High
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
4.5.4
Affected version:
Difficulty:
uncategorized
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Description

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.

1GUJ_AB_atoms.pdb (32 KB) 1GUJ_AB_atoms.pdb coordinate file to be used as a test case Justin Lemkul, 07/21/2011 05:48 PM

History

#2 Updated by Berk Hess about 8 years ago

  • Assignee changed from Berk Hess to Erik Lindahl

#3 Updated by Rossen Apostolov about 8 years ago

  • Priority changed from Normal to 6

#4 Updated by Rossen Apostolov about 8 years ago

  • Status changed from New to 3

#5 Updated by Rossen Apostolov about 8 years ago

  • Status changed from 3 to Closed

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