[gmx-users] pdb file for ammonia

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 31 22:34:45 CET 2009

nishap.patel at utoronto.ca wrote:
> Does anyone know where I can get a pdb file for ammonia? I tried 
> searching but I am not sure if there is a website for the pdb files I 
> can use in gromac. Any suggestions would be helpful.

For something simple like ammonia, you could probably just write the coordinates 
from basic geometry.  Failing that, parse out the coordinates of an 
appropriately-protonated lysine residue in a protein structure.


> Thanks.
> Nisha


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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