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Bug #412

possible pdb2gmx problem?

Added by Abdullah Ahmed over 9 years ago. Updated over 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

Hi.

I was having some trouble with the C-terminus in a structure I was using.
It was not working with pdb2gmx.

After posting this questions to the forums, I got the following suggestion, and it worked.

In ffencadv-c.tdb, I think there is a typo (even in the latest version of
Gromacs). Make a copy in your working directory and change the following lines
from:

[ dihedrals ]
N CA C O1
[ impropers ]
O2 CA C O1 improper_X_X_A_X

to:

[ dihedrals ]
N CA C O
[ impropers ]
OT CA C O improper_X_X_A_X

Let me know what kind of files you need.

History

#1 Updated by David van der Spoel over 9 years ago

I have implemented your suggestion, but in the latest git sources there are more changes to the files which make that terminal oxygens are converted to OXT first (which is common in pdb files). This is however not supported in this force field (it could be, but I don't know what charges one would have to use). Right now the encad force fields are not usable. If you would be willing to provide patches for the latest git source that would be appreciated.

#2 Updated by Berk Hess over 9 years ago

I fixed this for the 4.5 release.

Note that we would not suggest to use the encad force fields.

Berk

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