Quoting WanJ Ding <strollingforever.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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Received on Wed Jun 18 2008 - 06:07:48 PDT
