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
