Hi François,
Thank you very much, I'll try that. Just one thing: I understand that
R.E.D can help with the charges, but what about the
bonds/angles/dihedrals? Can I combine R.E.D. results to, say,
antechamber's to get those?
Thanks,
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
On Fri, May 20, 2011 at 4:55 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Gustavo,
>
>> I need to parametrize a ligand that is a tripeptide blocked with
>> terminal groups that are not available in the Amber parameter
>> database:
>>
>> Boc-Gly-Arg-Arg-AMC (see:
>> http://www.chemexper.com/chemicals/supplier/cas/113866-14-1.html)
>>
>> Where:
>> Boc = t-butiloxy-carbonyl
>> AMC = 7-amine-4-methyl-coumarin
>>
>> Could someone suggest what would be the best way to do it? I
>> considered just using antechamber for it, but since the amino acids
>> are available in the regular force fields, I imagine it could be best
>> to just use those parameters for the amino acids. Is that correct? If
>> this is the case, what would be the best procedure to parametrize the
>> terminal groups? What should I do to ensure a good description of the
>> bonds/angles involving both terminal group and amino acid atoms?
>
> Your two chemical groups are new capping groups: you could define
> intra-molecular charge constraints (INTRA-MCC keyword in a P2N file)
> set to zero in the two corresponding P2N files for the NHMe or COMe
> capping groups.
>
> You could test the following models:
> tert-butyloxycarbonyl-NHMe
> 7-amine-4-methyl-coumarin-COMe
>
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
>
> If you decide to use R.E.D. Server, the statistics module of R.E.D. IV
> will directly report the differences between the charge values
> generated without and with the intra-molecular charge constraint for
> each molecule.
>
> I hope this helps.
>
> regards, Francois
>
>
>
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Received on Fri May 20 2011 - 03:00:03 PDT
