AMBER Archive (2005)

Subject: Re: AMBER: Question about GAFF atom types

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Fri Jun 17 2005 - 17:31:52 CDT


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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