Re: [AMBER] Non-standard residue parameterization questions

From: Matthew Guberman-Pfeffer <>
Date: Sat, 1 Jan 2022 12:39:09 -0500

I just want to append to this thread some additional comments for any future reader:

1) As Anselm suggested, the discrepancy between my computed RESP charges and the standard ff14sb charges was almost entirely due to the dependence on confirmation. To account for this aspect, I performed a multi-conformational RESP fit for 1652 conformers of Tyr (capped by ACE and NME). The conformers were taken from the particular Tyr in the protein system I plan on mutating. I figured conformers fairly close to the ones sued in the original charge derivation may be among the distribution of states sampled from the MD with those charges. The charges I now obtain all fall within 0.08 of the original charges, which is significantly better than before.

2) I found helpful the discussion of charge derivation in Robalo et al., "The Multiple Origins of the Hydrophobicity of Fluorinated Apolar Amino Acids” Chem, 2017, 3, 881–897.


AMBER mailing list
Received on Sat Jan 01 2022 - 10:00:02 PST
Custom Search