Re: [AMBER] Error and sudden halt in equilibration

From: Stephan Schott <>
Date: Fri, 22 Feb 2019 15:21:32 -0300

Hi senal,
If you parametrized things with gaff2, probably you are on the safe side
with respect to hydrogen radii. You can check it nonetheless like Bill
suggested or with parmed (check the print commands). Now, I also had some
issues myself parametrizing a fructose ring with gaff2, as one hydrogen
collapsed into one of the carbons next to the ether of the ring, causing
the issues in my simulations. I didn't spend too much time debuging the
parameters (as it took me long enough to catch exactly a frame where things
went bonkers), but I think one of the dihedrals was off. I ended up using
GLYCAM, and no more issues, so I would recommend you either do the same, or
fine-tune your parameters if you identify what part of the molecule blows
up (with paramfit for example).
Hope it helps,

El vie., 22 feb. 2019 a las 2:49, Bill Ross (<>) escribió:

> > Would you mind telling me as to how to check for Lennard-Jones
> parameters specifically for Hydrogens?
> 1. List the atom types in the ligand, using either 'desc LIG' in leap,
> or look directly at the lib file.
> 2. See if any (h's most likely) don't appear in the other ligands.
> 3. Report any such cases here, optionally figure out which ff file
> defines the gaff atom types, and see what 'R*, epsilon' are for
> that/those type(s).
> Bill
> _______________________________________________
> AMBER mailing list

Stephan Schott Verdugo
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
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Received on Fri Feb 22 2019 - 10:30:02 PST
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