Re: SSBonds and charge problems

From: David A. Case <case.scripps.edu>
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

-- 
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David A. Case                     |  e-mail:      case.scripps.edu
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Received on Sat Apr 12 2003 - 06:53:01 PDT
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