[gmx-users] pdb file for ammonia

[chris.neale at utoronto.ca]

Hi Nisha,

Hetero-Atom Navi is a collection of heteroatoms culled from the PDB.
http://hetpdbnavi.nagahama-i-bio.ac.jp/index.php?mode=0

However, having only one heavy-atom, ammonia is unlikely to be  
usefully extracted from this resource for use in atomistic MD.

You can easily make it yourself by taking some protein, running it  
through pdb2gmx -ignh -ter and taking the NH3 terminal group  
coordinates as your ammonia coordinates.

This all assumes that you have some topology for ammonia, else the  
structure will do you little good.

Chris.

-- original message --

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.

Thanks.

Nisha