AMBER Archive (2003)

Subject: Re: waterbox

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Fri Mar 21 2003 - 17:33:31 CST

For the Amber reflector database:

The system was HUGE, Amber6/Leap put the atom number/residue numbers in the
wrong columns. Shifting the fields revealed that the PDB file was fine.
This is a known problem in Amber6.

jim

On Fri, 21 Mar 2003, GUILLERMINA L ESTIU wrote:

> amber6, tleap. The water box IS discontinuous, with the water molecules
> arranged in a big square and a long rectangle on the side.
> I can send you the pdb file, if you want
> Leap did not complain. Everything seems to be fine until you look at the pdb .
>
> On Fri, 21 Mar 2003 14:31:07, caldwell_at_heimdal.compchem.ucsf.edu wrote:
>
> >
> > You need to be more specific: a) amber version? b) did LEaP complain about
> > anything? c) do you mean the water is "discontinuous"?
> >
> > jim
> >
> >
> > On Fri, 21 Mar 2003, GUILLERMINA L ESTIU wrote:
> >
> > > I am trying to build a waterbox for a protein that has 1586 residues (24220
> > > atoms)
> > > Whem I succeed in building it, it looks funny, with rectangles of water at
> the
> > > sides of the protein.
> > > Has anyone faced this problem before?
> > > There is no problem with a watercap
> > > Dr Guillermina Estiu
> > > Chemistry Department
> > > Pennsylvania State University
> > > PA 16802
> > >
> >
> > --
> >
> > ----------------------------------------------------------------------------
> > 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
> > ----------------------------------------------------------------------------
> >
> >
> >
>
> Dr Guillermina Estiu
> Chemistry Department
> Pennsylvania State University
> PA 16802
> 

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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
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