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: case.scripps.edu
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:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Sat Apr 12 2003 - 06:53:01 PDT
