AMBER Archive (2005)

Subject: Re: AMBER: Question about GAFF atom types

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Jun 17 2005 - 15:42:18 CDT

Dear Herbert,

Check out the AMBER tut. #5 of the 2005 AMBER Workshop.
http://www.psc.edu/biomed/training/workshops/2005/Amber/psc_workshop/Tutorial_five/index.htm

This tutorial is about antechamber, which will automatically predict the
bond types and the needed parameters. If you know any experimental results
for your structure (such as the bond length, bond angle, etc.) you can
modify the frcmod file which will be created by this tutorial. Other than
this, it will be very hard to create your own parameters. The best way to
do is to compare with the other structures, and use those parameters for
your system. Hope this helps.

Good luck...

On Fri, 17 Jun 2005, Herbert Georg wrote:

> In fact here N is more like an N+.
>
> Herbert Georg wrote:
>
> > Hi, I'm trying to find the best choice of parameters to apply to a
> > sistem like
> >
> >
> > CH3
> > \
> > N == quinone
> > /
> > CH3
> >
> > I'm specially worried about the N, which is an amine N and makes 2
> > bonds with a quinone ring. I'm worried also about the quinone carbon
> > with which the nitrogen bonds. I looked at the J. Comp. Chem. article
> > and also inside the parameter's file, gaff.dat, but couldn't decide
> > for the pair of atom types. For example If I set the N atom as "nh"
> > and the C atom as "c", I noticed that there are no parameters for the
> > bond c-nh. Any light on this would be wellcome.
> > Thanks,
> > Herbert
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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