AMBER Archive (2008)

Subject: Re: AMBER: about resp charges

From: wanjian ding (dingwanjian_at_gmail.com)
Date: Wed Jun 18 2008 - 15:43:35 CDT

so, there is no ready resp charges for these atoms?

anyway, i thanks you so much. i will try as you told me.

Best
Stroll

2008/6/17 FyD <fyd_at_q4md-forcefieldtools.org>:

> Quoting WanJ Ding <strollingforever_at_gmail.com>:
>
> I am a new user of amber.
>> I am trying to get the resp chagres of every atoms in
>> tert-butyloxycarbonyl
>> (boc) group. The other paprameters could be found in gaff, but I don't
>> know
>> where I could find the corresponding resp charges. Could anyone help me?
>>
>
> I think you need to compute the RESP charge values for the molecule:
> tBoc-NHMe
> and you use an intra-molecular charge constraint (INTRA-MCC) sets to zero
> for the NHMe group (NME).
>
> This is straighforward using R.E.D.
> See for instance the tutorial http://q4md-forcefieldtools.org/Tutorial/
> and in particular:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10 Scheme 1
>
> As you can see in Scheme 1 two INTRA-MCC are used to generate RESP charge
> values for the central fragment of a new amino-acid. In your case, you could
> follow a similar strategy but using a single INTRA-MCC such as:
>
> t-Boc-NHMe --R.E.D.-III--> charge values within a force field library
> <--> (Tripos mol2 file format):
> INTRA-MCC = 0 - whole molecule: tBoc-NHMe
> - molecule fragment: tBoc
> (what you really need)
>
> If you are interested I can run your charge value derivation and force
> field library generation using the beta version of the R.E.D.Server
> (interface of R.E.D.-IV) we are going to release. It should take 2 minutes
> ;-)
>
> regards, Francois
>
>
>
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