AMBER Archive (2008)

Subject: Re: AMBER: about gaff.dat in ambeTools 1.0

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Jun 24 2008 - 08:37:09 CDT

Alan,
The cz atom type in antechamber1.27 was used to do a test (how corresponding
atom types work and how improper dihedral term affects the calculation
result). It should be removed.

Best

Junmei

On Wed, Jun 18, 2008 at 9:44 AM, Alan <alanwilter_at_gmail.com> wrote:

> Dears,
> Is there any special reason why this:
>
> diff amber10/dat/leap/parm/gaff.dat antechamber-1.27/dat/leap/parm/gaff.dat
> 16a17
> > cz 12.01 0.360 Sp2 carbon in guadinium
> 5030a5032
> > X -X -cz-X 10.5 180. 2. Just for
> guadinium, Junmei 2006
> 5109a5112
> > cz 1.9080 0.0860 OPLS
>
> I.e., why references to 'cz' disappeared for gaff.dat in amberTools 1.0
> once they was there for AC 1.27?
>
> Cheers,
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
>

-----------------------------------------------------------------------
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