Parameterizing a novel peptide

From: Bryan Roessler (
Date: Fri Sep 11 2015 - 17:14:05 CDT


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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