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Bug #319

segmentation fault from grompp with non-existing atomtype in *.top

Added by Maarten Wolf over 11 years ago. Updated over 11 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

When generating input for free-energy perturbation I set the B atomtype to DUM in my topology file. However DUM does not exist in the force field I wanted to use. In version 3.3.3 this resulted in an error message (as expected).
In version 4.0.4 I got a segmentation fault (which should be an error message).

min0.00.mdp (798 Bytes) min0.00.mdp mdp file for energy minimization of Thymine in vacuum Maarten Wolf, 05/19/2009 10:59 AM
BugTest.tgz (32.7 KB) BugTest.tgz tar containing amber force field files, a energy minimization mdp, Thymine gro and Thymine top with atomtype DUM (non-existing in ffambersb). Maarten Wolf, 05/19/2009 11:04 AM

History

#1 Updated by David van der Spoel over 11 years ago

Please provide input files that work in 3.3.3 and not in 4.0.[45]

#2 Updated by Maarten Wolf over 11 years ago

Created an attachment (id=370)
mdp file for energy minimization of Thymine in vacuum

#3 Updated by Maarten Wolf over 11 years ago

Created an attachment (id=371)
tar containing amber force field files, a energy minimization mdp, Thymine gro and Thymine top with atomtype DUM (non-existing in ffambersb).

#4 Updated by Berk Hess over 11 years ago

There was only a check for the A-state atom types, not for the B-state.
I fixed it for 4.0.6 and 4.1.

Berk

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