AMBER Archive (2004)

Subject: Re: AMBER: About Disulfer bond

From: David A. Case (case_at_scripps.edu)
Date: Sat Nov 27 2004 - 12:05:28 CST

On Sat, Nov 27, 2004, Xiao He wrote:

> When I do optimization using sander program,the disufer bond(in CYX) will
> from 2.0 A(experiment results in pdb files)
> to 3.2-3.5A.
> What's the problem?

Did you add the bonds manually in LEaP (using the "bond" command)? LEaP
will not automatically include these bonds, you have to do it yourself.

...dac

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