[gmx-users] Amber03ws includes an unexpected dihedral with atoms -C N CA CB
Ramon Crehuet
ramon.crehuet at iqac.csic.es
Wed May 17 12:04:20 CEST 2017
Dear all,
I would like to use the Amber03ws force field described in Best, Zheng and Mittal, J. Chem. Theor. Comput., 10, 5113-5124, 2014.
This force field is contributed in http://www.gromacs.org/Downloads/User_contributions/Force_fields
When using it, Gromacs reports a warning about a CB atom in GLY residues. I could trace it to the aminoacids.rtp file, which contains these lines for the GLY residue:
[ dihedrals ]
CA C +N +H
O C +N +H
-C N CA CB
-C N CA C
CA C +N +CA
O C +N +CA
-C N CA HA1
-C N CA HA2
HA1 CA C +N
HA2 CA C +N
The presence of the CB atom is an error? Can I simply ignore this warining?
Thanks,
Ramon
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