Re: Parameterizing a novel peptide

From: Tomek Stępniewski (
Date: Fri Sep 11 2015 - 18:16:27 CDT

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 <>:

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

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