Angelo,
without having your actual files for inspection, I have to make a guess:
Probably in your prepin file, the residue definition contains an atom, which is not recognized by leap ("unknown element"), either because it is an element unknown to Amber up to now or because atom names/types/elements are mixed up. Thus have a closer look at your prepin file.
Next, the charge of -1 is not a problem, just a warning in case you setup a solvent simulation. If that the correct total charge of your group, it's ok. You'd get the same error, if a standard protein is not electrically neutralized.
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
________________________________________
Von: Angelo Gallo via AMBER <amber.ambermd.org>
Gesendet: Montag, 16. Dezember 2024 16:41:19
An: amber.ambermd.org
Betreff: [AMBER] Peptidoglycan
Dear AmberLists,
I tried to parametrize a Glycopeptide using Gaussian for the charges
calculations and the prepin generation instructions.
I have got this warning:
Leap added 1 missing atom according to residues templates:
1 unknown element
And
The unperturbed charge of the unit (-1.000000) is not zero.
What should I check?
It is a n-acetyl glucosamine and a modified muramic acid
Best
Angelo Gallo
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Received on Mon Dec 16 2024 - 08:30:02 PST
