[gmx-users] H211 in ffG53a5

[David Mathog]

> 
> I added the RNA hydrogens to my ffG53a5.hdb file, which eliminated the 
> H2*, etc. missing from .hdb file errors. 

1.  Use the Amber FF files instead.  (Requires some hand editing
of the PDB file.)

2.  Also build in my modifications to gromacs 3.3 from here

http://saf.bio.caltech.edu/pub/software/molbio/gromacs-cit-33.tar.gz

and you can probably just run your input PDB file through pdb2gmx
using the Amber FF with no hand editing required.

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech