AMBER Archive (2006)

Subject: Re: AMBER: loading torsion parameters

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Mon Jul 31 2006 - 15:35:18 CDT

Thanks Ross,
     I did what u suggested but it gave me a warning:

 WARNING: expected Improper Torsion PK>0 (-2.820000)
 WARNING: expected Improper Torsion PHASE=180 (0.000000)

for all the four torsions. I was just wondering if these are some
harrmful warnings or I can neglect them. I took them from ur thesis.
Have there been updates in the parameters that you published in your
thesis? I also have 4 CYM coordinating a zinc atom.

thanks a lot in advance,
sincere rgds,
Nitin

On 31/07/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Dear Nithin,
>
> > CC-NB-ZNA-SH -2.82 0.00 2.0
> > CR-NB-ZNA-SH -2.82 0.00 2.0
> > SH-ZNA-SH-CT -0.03 0.00 2.0
>
> You need to include the 'divisor' for the dihedral terms. In your case these
> are all unique dihedrals (I.e. don't include degenerate systems such as
> methyl groups) and so a value of 1 is fine. I.e.
>
> CC-NB-ZNA-SH 1 -2.82 0.00 2.0
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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