[gmx-developers] pdb2gmx

[Tsjerk Wassenaar]

Hi Ran,

> 2. How difficult is it to implement the possibility to choose (by the
> user or automatically) which OD atom to protonate for ASPH or GLUH?
> Right now it's not compatible with the FF files, but this is not the
> main issue I guess.

Of course that's just a matter of exchanging coordinates. I have a
script doing that following checking with WHATCHECK. Of course, having
pdb2gmx dealing with it would have some merits.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623