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Bug #576

genbox mixes residue names for mixed solvent box

Added by Krzysztof Kuczera about 9 years ago. Updated about 9 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

I have copied a urea + water box urea+h2o.gro from an older distribution of GROMACS and am trying to solvate a peptide with it. Either solvating a peptide or just replicating the box produces a coordinate file
with misnamed residues. Here is a sample command:

~/prog/gromacs-4.5.1/bin/genbox -cs urea+h2o -box 3 3 3 -o urea+h2o333

the urea+h2o333.gro file looks OK on graphics, but the residue names are mixed - some urea molecules
are named 'SOL' and some water molecules are named 'URE'. Also, when solvating the peptide, the
.top file only shows that 680 SOL molecules were added, not how many URE and SOL ...

I attach the input urea+h2o.gro coordinate file

Krzysztof Kuczera

History

#1 Updated by Roland Schulz about 9 years ago

Berk,

you introduced this bug with commit 1d80ebe46cb2b71453bd2a8c3401dd60c9759add

#2 Updated by Berk Hess about 9 years ago

Thanks for the tip, Roland!

I fixed it with commit: cde612c06b8de8d1835a1bdbb87b6725f913b644

The results with this old version should have been correct,
except for the residue names. After grompp (-maxwarn 1) that should
have been correct as well.

Berk

#3 Updated by Berk Hess about 9 years ago

Forgot to resolve.

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