Re: SSBonds and charge problems

From: <>
Date: Fri, 11 Apr 2003 12:50:04 -0700 (PDT)

Disulfide bonds are NOT automatically recognized/created by
leap, you have to put them in by hand using the "bond"
command before you "saveamberparm".


On Fri, 11 Apr 2003, Steve Seibold wrote:

> Hi
> 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?
> 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?
> Thanks, Steve

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-514-3866  
UCSF Box 2240                             (email)
600 16th Street
University of California
San Francisco, CA 94143-2240
Received on Fri Apr 11 2003 - 20:53:02 PDT
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