Re: SSBonds and charge problems

From: David A. Case <>
Date: Fri, 11 Apr 2003 22:29:53 -0700

On Fri, Apr 11, 2003, Steve Seibold wrote:

> I am experiencing some problems with my disulfide bonds. When I start
> out at 0.00 time, I have disulfide bonds(CYX), but after just 125 fs
> they break and separate. Why is this?

Make sure you use the "bond" command to add the bonds -- it is not enough
just to make the residue be CYX.

> Another problem I have is that in leap when I load my protein, it tells
> me that it has zero unperturbed/perturbed charges without any addition
> of counter ions or water. Why is this?

What is the correct charge supposed to be? You can use ambpdb to print
out the charges -- maybe that will help you find anything that is not what
you want it to be.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Sat Apr 12 2003 - 06:53:01 PDT
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