[gmx-users] Glycine zwitterion parameters in Amber FF

[Pelin S Bulutoglu]

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?


Regards,

Pelin Su Bulutoglu

[Justin Lemkul]

Post by Pelin S Bulutoglu
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
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Justin A. Lemkul, Ph.D.
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