On Oct 25, 2010, at 10:01 AM, Michela Candotti wrote:
> Hi,
> I'm trying to use tleap (amber 9) to solvate a protein in a Urea-Box using
> the standard parameters in tleap (8Mureabox.off and frcmod.urea) but I guess
> that there is a problem with the box dimension. When I visualize the outputs
> (using VMD) I can clearly see some empty space between the solvent-boxes
> that are added (i.e I can see a sort of cross-like empty shape between the
> 4 boxes that are added to solvate the entire protein, with the protein in
> the center ).
>
> This is the procedure:
>
> loadoff 8Mureabox.off
> loadamberparams frcmod.urea
> x = loadpdb test.pdb
> solvatebox x UREABOX 12
> saveamberparm x xx.top xx.crd
>
> I've tried to change different parameters and I guess that the problem is in
> those ones in the 8Mureabox.off file:
> !entry.UREABOX.unit.boundbox array dbl
> 1.000000
> 1.570797
> 46.25620
> 43.05300
> 49.13420
>
> If I change the box size , the last three number in the list, (according to
> the vmd "measure minmax") I can slightly reduce the empty-space but it is
> still present.
> Anyone has an idea about how solve this problem?
>
> Thanks
>
>
> Michela Candotti
> IRB Barcelona
Gaps between the boxes used by tleap to solvate are known and expected (due to
the tleap algorithm). You must equilibrate the density with constant pressure
(at least) before production dynamics.
HTH,
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Mon Oct 25 2010 - 08:30:05 PDT
