AMBER Archive (2008)

Subject: Re: AMBER: A problem of dihedral angle

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jun 25 2008 - 10:53:16 CDT

each carbon probably has a dihedral term to help it stay planar.
the program that assigns these depends on how you got the parameters
for benzene, it could be leap or antechamber.

On Wed, Jun 25, 2008 at 11:31 AM, Harry (Yicun) Ni <edycni_at_gmail.com> wrote:
> Hello,
>
> I'm using Amber to calculate the energy of benzene. In the output, there are
> two parameters which are
> 'NPHIH=24' and 'NPHIA=6'. Does it mean that the total number of dihedral
> angles in benzene is 30?
> However, the program in our group for internal use shows that the total
> number of dihedral angles in
> benzene is 24. I counted manually and think 24 should be correct. (for every
> C-C bond there are 4 dihedral
> angles). So, could you help me on this problem? Also, could you tell me
> which source files in Amber
> generate the dihedral angles and assign the parameters? Thank you very much.
>
> Harry @ ucf.chem
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu