AMBER Archive (2004)

Subject: RE: AMBER: Sander : Vrand flag

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Tue Aug 31 2004 - 09:15:37 CDT

Hi Amber Users,
Yes,
 As Ross had said,indeed the loss of solvent cap
information was an isssue.I tried adding the water
molecules first and then the watercap. The simulation
went through just fine.
 By the way I dont if there is anyway so that one can
preserve the cap information after loading the
modified pdb file in to xleap again.
 If anyone has any experience please share.

Regards
Sachin Patil
--------------
Graduate Student
Dept. of Medicinal & Biological Chemistry
University of Toledo, Toledo
Ohio 43606

 --- "Furse, Kristina Elisabet"
<kristina.e.furse_at_vanderbilt.edu> wrote:
>
> > (Interestingly, with another system which has no
> manually added water
> > molecules the simulation goes fine. Eventhough the
> temperatures and high,
> > similar to above.)
>
> Just a little note on this comment. It may be that
> in the process of
> transforming your initial system into a pdb,
> manually adding more water and
> reading back into leap, you lose your solvent cap
> information (the restraining
> directions, not the waters themselves), and
> therefore see the water boil off.
> I've never worked with caps, but the above is true
> for periodic boxes (in
> amber7, anyway). Once you go to pdb (no box or cap
> info), then back into leap,
> you need to reset the box info. Anyway, Ross'
> suggestion that you manually add
> waters first, then set up the cap should take care
> of this as well if it is an
> issue.
>
> Kristina
>
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