Re: [AMBER] Parametrization of new amino acid in methanol solvent

From: Alessandro Contini <>
Date: Fri, 19 Jan 2018 14:03:50 +0100

Dear Chetna,
actually the charge parameterization of Amber ffs (those derived from
the parm9X series, so all ffs up to ff14SB, but not the ff03) is done by
QM calculations at the HF-6-31G level in the gas phase. This because it
has been observed that a good representation of the electrostatics in
solution is obtained by some sort of error cancellation.
So, it is not needed to reparameterize your non-standard AA in methanol
(otherwise you should also reparameterize the whole ff). If you want a
better correlation to experiments (i.e. NMR), it is enough to carry your
MD simulations in explicit methanol.

Good luck for your simulation


Il 19/01/2018 13:10, Chetna Tyagi ha scritto:
> Dear all,
> I study a fungal peptide with non-standard residues like AIB, and
> D-isovaline etc. I parametrized them using R.E.D server and used for
> simulations in explicit water and methanol solvents.
> I was recently advised that I should carry out the parametrization and
> charge calculation of these residues in methanol solvent for accuracy. Is
> it possible using R.E.D server? Because I searched through and I could not
> find any such information.
> Has anyone attempted to do it before? Is there a way in Amber to add
> various solvent effects during parameterization?
> Any help would be much appreciated.

Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
skype alessandrocontini
AMBER mailing list
Received on Fri Jan 19 2018 - 05:30:03 PST
Custom Search