AMBER Archive (2003)

Subject: Re: SSBonds and charge problems

From: David A. Case (case_at_scripps.edu)
Date: Sat Apr 12 2003 - 00:29:53 CDT


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_at_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 ==================================================================