[gmx-users] Glycine zwitterion parameters in Amber FF

Justin Lemkul jalemkul at vt.edu
Sat Dec 1 03:57:05 CET 2018

On 11/30/18 3:04 PM, Pelin S Bulutoglu wrote:
> Dear Gromacs users,
> I am working on simulating glycine zwitterions in solution and in solid form. I have been using parameters from GAFF to run my simulations. I would like to try other force fields that are available in the Gromacs database. However, when I tried using AMBER force fields (amber99 specifically), I get an error from pdb2gmx saying that there is no residue type in the force field for 'GLY' as a standalone residue. Is there a way to work this out without manually entering the parameters?

You'll have to define a new residue. AMBER force fields assign different 
charges to N- and C-terminal residues, so zwitterions will naturally be 
a special case.



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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