AMBER Archive (2005)

Subject: Re: AMBER: Question about GAFF atom types

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Jun 20 2005 - 14:51:59 CDT


The ring part of your system looks like the base part of RC (or DT). So,
the first thing that came to my mind is to use the atom types used in
RC/DT system. It also has 2 carbons bonded to oxygen. And in that system,
some of the carbons have atom type name CM. It is in parm99.dat. As I
said before, the best thing to do (if you dont want to find the
parameters for your system experimentally/computationally) is to find a
similar structure and use those atom types in your system.

On Mon, 20 Jun 2005, Herbert Georg wrote:

> What are the CB and CM atom types? I haven't found them in the gaff.dat
> parm file.
>
> Ilyas Yildirim wrote:
>
> >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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> >>>>
> >>>
> >>>
> >>>
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> >>
> >>
> >
> >
> >
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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