AMBER:

From: Beale, John <jbeale.stlcop.edu>
Date: Tue, 20 Feb 2007 07:02:24 -0600

I am trying to set up a protein for AMBER 9 using LEaP. I have used
SYBYL to initially view the pdb file and to remove the hydrogen atoms.
The protein has 7 intramolecular disulfide bonds. I find that if I just
use the pdb file as input to LEaP the .top and .crd files are written
using saveAmberParm. The problem arises when I try to bond the
disulfides in LEaP. When I do this LEaP gives me the following warnings:

 

Could not find bond parameters for: SH - SH

 

Could not find angle parameters for: HS - SH - SH

                                                     SH - SH - CT

                                                     SH - SH - HS

 

Could not find proper torsions. No torsion terms for : HS - SH - SH - CT

 
HS - SH - SH - HS

 
CT - SH - SH - CT

 
CT - SH - SH - HS

 

A total of 217 improper torsions applied.

 

The *.top and *.crd files are not generated when I do a saveAmberParm.

 

These parameters seem like nonsense to me. For instance, there are no SH
- SH bonds in the protein.

 

Can anyone give me some insight on how to work through this?

 

Thanks!

 

John Beale

 


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Received on Wed Feb 21 2007 - 06:07:41 PST
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