[gmx-users] pdb file for ammonia

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Dec 31 22:42:52 CET 2009

Hi Nisha,

Hetero-Atom Navi is a collection of heteroatoms culled from the PDB.

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.


-- 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.



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