AMBER Archive (2003)

Subject: Re: SSBonds and charge problems

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Fri Apr 11 2003 - 14:50:04 CDT

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

jim

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
>
> 

-- 

----------------------------------------------------------------------------
NOTE NEW MAILING ADDRESS & FAX NUMBER:

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-514-3866  
UCSF Box 2240                             (email) caldwell_at_heimdal.ucsf.edu
600 16th Street
University of California
San Francisco, CA 94143-2240
----------------------------------------------------------------------------