[gmx-users] Phenylglycine parametrization in OPLS

Ashutosh Jogalekar ajogale at emory.edu
Tue Mar 7 20:52:04 CET 2006

I am trying to parametrize an unnatural amino acid-phenylglycine  
(PHG)- in the OPLS force field in GROMACS for an MD simulation. In  
the ffoplsaa.hdb file, the following is the format for the hydrogen  
addition that I have put in:

1 1 N -C CA
1 5 CA N C CG
1 1 CD1 CG CE1
1 1 CD2 CG CE2
1 1 CE1 CD1 CZ
1 1 CE2 CD2 CZ
1 1 CZ CE1 CE2

As can be seen, I have added the correct tetrahedral hydrogen of  
type-5 in the second line (CA N C CG). Yet during the MD, the carbon  
fails to remain tetrahedral, with especially the hydrogen moving  
around a lot (it is staying bonded but the C CA H angle is getting  
highly distorted). What can I do to remedy this?
Thanks very much

Ashutosh Jogalekar
Emory University Chemistry Department

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