Re: Parameterizing a novel peptide

From: Mayne, Christopher G (
Date: Mon Sep 14 2015 - 08:48:57 CDT


I can't comment on parameterizing for AMBER, as I currently only work with CHARMM. In our opinion, the preferred method by far is a combination of the CGenFF Program (formerly ParamChem) to get a set of initial parameters (and to perform atom typing for you), followed by validation and/or refinements baesd on the penalty scores. We recognize that some users may not have access to Gaussian, and are attempting to address this limitation; however, support for an expanded set of QM software likely won't be available anytime soon (there are lot of software limitations to work around).

As for your technical question, my advice is to retain as much of the standard protein force field parameters as possible. I would use the divide and conquer strategy to parameter only the missing fragments. The problem then becomes largely a translation issue between the CGenFF atom types (if that's what you've parameterized the fragments in) and the CHARMM atom types (the peptide backbone). Both the CGenFF and CHARMM methodologies use the approach to computing partial atomic charges, so they should be compatible.

Christopher Mayne

Date: Sat, 12 Sep 2015 01:16:27 +0200
From: =?UTF-8?Q?Tomek_St=C4=99pniewski?= <<>>
Subject: Re: namd-l: Parameterizing a novel peptide

don't know anything about antechamber,
most of the people I know use ParamChem (and they get published), but
overwrite the charges they get from Gaussian, but if You don't do that I
suppose nobody's going to jail
best of luck:-)

2015-09-12 0:14 GMT+02:00 Bryan Roessler <<>>:


I know that the currently recommended way to parameterize a novel residues
'round these parts is to use the FFTK, unfortunately I do not have access
to Gaussian.

Is using antechamber and the built-in SQM MM program and GAFF considered
'good enough' for publication (assuming I'm using Amber FFs)? Or is using
pyRED server with Gaussian (and the appropriate composite method) for Amber
and/or CHARMM preferred?

I was excited to try to create GAMESS input files with VMD, but it does
not appear that the functionality is quite complete.

Lastly, I have technical question regarding parameterization. My peptide
of interest is 5 residues long: three standard amino acids flanked on the N
and C termini by a carboxybenzyl protecting group and a reactive sulfur
compound (both peptide bonds), respectively. Ideally I would like to use
the standard forcefields for the standard amino acids and only parameterize
the novel flanking residues. I have no problem parameterizing the novel
residues as stand-alone compounds, but then of course I am missing the
peptide bond parameters. How can I parameterize the peptide bonds but still
use the standard forcefields for the 3 amino acids in the middle of the
peptide? Do I need to parameterize the entire peptide and then cut and
paste the peptide bond parameters? I fear that may unfavorably mix partial
charges. I'm familiar with doing this in CGenFF but less so in Antechamber.

Thanks for your help,


*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
* <>*
Knowledge that will change your world


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