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Bug #1276

pdb2gmx ignores angles when no bonds are present

Added by Justin Lemkul over 4 years ago. Updated over 3 years ago.

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

As recently posted on gmx-users, pdb2gmx will not write angles if bonds do not connect the constituent atoms, despite being present in an .rtp [angles] directive. For most purposes, this is not a problem, but there are specialty force fields that need such behavior. I have attached a much simpler test case than the original gmx-users post to reproduce the problem. Invoke with:

echo 1 3 | pdb2gmx -f water.pdb
files.tgz (61.5 KB) files.tgz Justin Lemkul, 06/05/2013 06:03 PM

Related issues

Related to GROMACS - Bug #1711: gmx x2top seg faultClosed

Associated revisions

Revision 7ba0a841 (diff)
Added by Erik Lindahl over 3 years ago

Enable rtp angle/dihedral entries not connected by bonds

pdb2gmx has previously silently ignored any angles or
torsions not connected by bonds. This patch adds code
to mark with RTP/hackblock entries that have been
assigned in this search, and afterwards we add those
that have not yet been matched. In particular, this makes
it possible to have angles or torsions in RTP entries
even if those atoms are not connected by bonds.

Fixes #1276.

Change-Id: I61c3c3954ef8c4cd59956d88b73c6a69c1a66c65

History

#1 Updated by David van der Spoel over 4 years ago

  • Tracker changed from Bug to Feature

pdb2gmx is for biomolecules only. Acpype and friends can be used for GAFF etc.

#2 Updated by Justin Lemkul over 4 years ago

I agree that there are plenty of ways outside of pdb2gmx that can generate topologies, but when pdb2gmx silently ignores an otherwise properly formatted .rtp entry, I think there's still a problem worth fixing. Nowhere in the documentation does it say that pdb2gmx can only be used for biomolecules, it says that it reads a list of input files and writes a topology. If we need to be more specific about limitations, that's fine, but when input files are written correctly (with respect to what the manual says), the end user is going to assume that the outcome will be correct, but in this case, it is not.

#3 Updated by Erik Lindahl over 3 years ago

  • Tracker changed from Feature to Bug
  • Affected version set to 4.6

Agree with Justin that this is a bug - either in the implementation or documentation.

#4 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1276.
Uploader: Rossen Apostolov ()
Change-Id: I89731c05f259c8e120e38d5fb1ac57a86be25d7b
Gerrit URL: https://gerrit.gromacs.org/3680

#5 Updated by Rossen Apostolov over 3 years ago

I'm not sure how to fix the implementation, but I added a note to the documentation for now.

#6 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1276.
Uploader: Erik Lindahl ()
Change-Id: I61c3c3954ef8c4cd59956d88b73c6a69c1a66c65
Gerrit URL: https://gerrit.gromacs.org/3686

#7 Updated by Erik Lindahl over 3 years ago

  • Status changed from New to Fix uploaded

#8 Updated by David van der Spoel over 3 years ago

  • Status changed from Fix uploaded to Closed

#9 Updated by Teemu Murtola over 3 years ago

  • Assignee changed from David van der Spoel to Erik Lindahl
  • Target version changed from future to 5.0

#10 Updated by Rossen Apostolov over 2 years ago

  • Related to Bug #1711: gmx x2top seg fault added

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