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Bug #3048

Dihedral parameters for N-terminal in gromos53a6 force field in the aminoacids.n.tdb file with different values in versions 4.6.7 and gromacs 2019/2016/5.1.5

Added by Danilo Coelho 4 months ago. Updated 4 months ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
simple
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Description

Hi all,

I'm trying to perform a benchmark for different versions of Gromacs, because I've been facing some troubles with version 4.6.7 on the cluster I'm current using.

After performing the pdb2gmx on the same input pdb file, but using different versions of Gromacs, I could observe that the topology files created are identical,
except for the dihedral parameter for the N-terminal atoms H1-N-CA-C, which is stated as gd_39 in the newer versions (2019/2016/5.1.5), whereas for version 4.6.7 it is gd_29.

Taking a look at the aminoacids.n.tdb file for gromos53a6 ff, you can find that's actually a different parameter for those atoms in different version.

Is that a change in the nomenclature or a bug?

Thank you for all the help,
Danilo.

History

#1 Updated by Paul Bauer 4 months ago

This was a bug in the older versions (#1022) that got fixed in 05efeff756b

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