Re: [AMBER] parameter-for-peptide-blocking-group

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Fri, 06 May 2011 16:35:54 +0200

Dear vhakkim boy,

> Is there any amber ff parameter for peptide-blocking-group
> like OMe, t-BOC , because my sequence is {OMe-X-X-X-X-t-BOC}

You could follow an approach as in
http://q4md-forcefieldtools.org/REDDB/projects/F-85/ but obviously not
for sugars but for amino-acid and pseudo-dipeptide.

See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
This can be easily done in a single step using R.E.D. III.4 from the
R.E.D. III.4 tools or using R.E.D. Server.

regards, Francois



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Received on Fri May 06 2011 - 08:00:03 PDT