Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Tue, 03 Mar 2015 10:31:34 +0100

Dear Tao,

See http://q4md-forcefieldtools.org/REDServer-Development/
  and its tutorial:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php

and particularly:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#17
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#18

in agreement with:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract

regards, Francois

> I am doing simulation on system that with various compounds bonded to the
> N-terminal of certain peptide, like shown in the following picture. Now I
> am facing the problems with creating unit for such N-Cap residue.
>
> ?
> 1. Should I treat R1 combined R' as a N-Cap residue or just the R' only?
> 2. In any case above, is there any method available to assign correct
> partial charge and atom type for such non-standard residue?



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Received on Tue Mar 03 2015 - 02:00:03 PST
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