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
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Received on Mon Oct 25 2010 - 08:30:04 PDT
