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Bug #526

trjconv option inconsistency

Added by Mark Abraham about 9 years ago. Updated about 9 years ago.

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

trjconv sometimes requires a supporting input file with -s. trjconv -h supposedly permits .pdb and .gro files, however "trjconv -f in.pdb -o out.pdb -s support.gro -pbc cluster" segfaults.

Either calc_pbc_cluster needs to check whether t_topology is NULL and exit more gracefully, or earlier

if (0 == top.mols.nr && (bCluster || bPBCcomMol)) {
gmx_fatal(FARGS,"Option -pbc %s requires a .tpr file with -s", bCluster ? "cluster" : "mol");
}

since I suppose -pbc mol has this property too.

git head and 4.0.7 both have the faulty behaviour.

History

#1 Updated by Erik Lindahl about 9 years ago

Fixed in commit 893d1ce126d6ea52859eea9441df2971f7924835 for release-4-5-patches. This might not make it into beta4, but it's there for the final release.

I don't think we'll fix it in 4.0 since 4.5 should be out early next week :-)

#2 Updated by Peter Kasson about 9 years ago

This patch actually breaks trjconv -pbc mol for me (using older tpr's). Can you test it on your install? Right now, I get the error message when I run trjconv -s frame0.tpr -f run_cat.xtc -pbc mol -center -ur compact -o run_center.xtc using the current 4-5-patches. If I pull back to an older trjconv, everything works fine.

#3 Updated by Berk Hess about 9 years ago

I fixed it properly.

Berk

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