Re: Parameterizing a novel peptide

From: Mayne, Christopher G (
Date: Mon Sep 14 2015 - 21:38:04 CDT


It's been awhile since I've gone through the specifics, but to my knowledge, GAMESS cannot do dihedral scanning to construct relaxed potential scans. I also don't recall if GAMESS supports calculation of the Hessian using redundant internal coordinates, which is a required for optimizing bonds and angles. So, I don't think that it's just a manpower issue; there are some missing features.

Christopher Mayne

On Sep 14, 2015, at 9:08 PM, Peter Freddolino wrote:

> Hi Christopher,
> I’ve always wondered about this a bit — what is gamess missing that prevents it from being used as the main qm engine in fftk? Aside from writing differently formatted config files it should have all of the needed features, no? I understand if this is just a manpower issue, but if it is, maybe someone in the community who has need for the feature could be interested to help…
> Best,
> Peter
>> On Sep 14, 2015, at 9:48 AM, Mayne, Christopher G <> wrote:
>> Bryan,
>> 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.
>> Regards,
>> 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
>>> Hmm,
>>> 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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