AMBER Archive (2005)

Subject: Re: AMBER: Question about GAFF atom types

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Jun 17 2005 - 20:29:24 CDT

It is better to compare the structures and use similar atom types, then.
First that came to my mind is the following atom types:

   H1
   | H? O
H1-CT-H1 \ /
     \ CM-C
       \ / \
        N*-CB CM-H?
       / \ /
     / C-CM
H1- CT-H1 | \
    | O H?
    H1

The H? can be HA. I just checked out the atoms and which atoms they are
bonded. For instance, O bonded to C is always "O" type, and the C
bonded to this O is always "C" type. But as I said this is just a guess.
The bong length, bond angle, potential barriers... and dihedral angles.
These needs to be defined. If there are not any force field parameters for
this structure defined in the literature, and if you want to make a good
guess, I would suggest you to compare the structure with the known ones,
and define the missing parameters. Good luck...

On Fri, 17 Jun 2005, Herbert Georg wrote:

> I've tryied antechamber, but it sets wrong atom types ("ca" as if it
> were a normal aromatic ring) to the atoms in the quinone ring. I
> suppose, by reading the article, that the correct atom types for the
> inner carbon atoms in a quinone ring is "cc" and "cd". Thats why I'm
> trying to do it by myself.
>
> Ilyas Yildirim wrote:
>
> >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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> >
> >
> >
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
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