On Tue, 28 Sep 2010 13:21:45 +0530
hirdesh kumar <hirdeshs8.gmail.com> wrote:
> Hi,
> I have done the distance measurement analysis. The distance is always
> greater than 3 angstrom (suggesting that there is no disulfide
> bond:2.05 angstrom).
> Is there any way via which i can make the distance between two atoms
> rigid for the starting minimization and equilibration.
Have you confirmed that the S-S bond is indeed defined in your topology
file? With vmd you can try 'vmd -f -parm7 foo.top -crd foo.crd'.
This will force vmd to show defined bonds rather than from a heuristic
analysis. If it is defined then you better look into the actual cause
for the large deviation.
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Received on Tue Sep 28 2010 - 01:30:03 PDT
