Dear Prof.Case,
Thank you very much for your answer.
Best,
Xioling
> Date: Sat, 10 Jul 2010 09:52:48 -0400
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] same dihedral with different parameter in FRCMOD file
>
> On Sat, Jul 10, 2010, Xioling Chuang wrote:
>
> > I used gaussian output to generate forcefield parameters using
> > antechamber in AmberTools 1.3. My molecule is a DNA analogue. In frcmod
> > file I got the same dihedral with different values of parameters, some
> > part of frcmod file is listed below.
> >
> >
> > CT-N*-CM-H4 1 0.625 180.000 2.000 same as X -c2-na-X
> > CT-N*-CM-CM 1 0.625 180.000 2.000 same as X -c2-na-X
> > CT-N*-C -NA 1 1.450 180.000 -2.000 same as X -c -na-X
> > CT-N*-C -NA 1 0.350 180.000 4.000 same as X -c -na-X
> > CT-N*-C -O 1 1.450 180.000 -2.000 same as X -c -na-X
> > CT-N*-C -O 1 0.350 180.000 4.000 same as X -c -na-X
> >
> > Since this is one molecule, is it possible to get the same dihedral with
> > different parameters (lines 3 & 4, as well as lines 5 & 6)?
>
> Yes, this is normal. Many dihedrals have multiple parameters. In you
> examples, one of the terms has n=2, the second has n=4. The sum of these
> two Fourier terms is the full potential. You will see lots of such examples
> in a "regular" parm.dat file, such as parm99.dat
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_________________________________________________________________
Your E-mail and More On-the-Go. Get Windows Live Hotmail Free.
https://signup.live.com/signup.aspx?id=60969
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 11 2010 - 07:00:03 PDT
