Date: Mon, 16 Dec 2002 12:37:46 -0600
From: Thomas
Subject: Re: solvating a protein with large cavity

Yeup, that helped do it but only 9 waters ended up in the cavity
which is about 500A^3. This is less than what I expected, but maybe
close enough.
Granted, i expect the "structure" of the waters to be a bit different
from
the bulk water that WATBOX216 represents so who knows how many should
really be in
there.


Here's what I finally worked out to get the waters put in, where
{27.7 25.9 35.4} is the center of the cavity

solvatecap REC WATBOX216 { 27.7 25.9 35.4 } 12 .75

solvatebox REC WATBOX216 6



Can you tell me the proper tleap syntax for the following:
If I know what resiudes bound the cavity,
how do I calculate the center of mass of these
amino acids and feed it to solvatecap as an arguement.
All the ways I tried doesn't work.


In general if there are small cavities in a protein would it make sense
to solvate it in two stages. Stage one try to gets waters in the
cavities with a reducued closeness
parameters and then stage 2 add bulk waters.

Suggestions on what combination of solvatebox, solvatecap, solvateshell
to use for such
a two stage watering?


Thanks,
TOm


"David A. Case" wrote:
>
> On Sat, Dec 14, 2002, Tom Bishop wrote:
>
> > I'm trying to solvate a protein w/ a large cavity (~500A^3) using tleap
> > in amber7.
> >
> > source leaprc.ff99
> > REC = loadpdb pro.pdb
> > solvatebox REC WATBOX216 6
>
> Does it help to reduce the closeness parameter? e.g.:
>
> solvatebox REC WATBOX216 6 0.7
>
> ..dac
>