This shouldn't happen. My first guess is that somewhere in your non-bonded
parameters (ALD perhaps?) you have a LJ parameter that is too small. First
confirm that your parameters are reasonable.
You can do this by hand or load the prmtop/crd into VMD (or other
visualization software), change to VDW view and see if the sphere sizes
look right.
-Dan
On Fri, Jan 6, 2012 at 2:07 AM, Gonzalo Jimenez Oses <gjimenez.chem.ucla.edu
> wrote:
> Dear all,
>
> I'm trying to solvate a big protein with a DMSO box downloaded from
> http://www.pharmacy.manchester.ac.uk/bryce/amber#box using tleap. This is
> what I do:
>
> **************
> source leaprc.ff99SB
> source leaprc.gaff
> loadoff dmso.off
> loadamberparams frcmod.dmso
> loadAmberPrep ALD.prepin
> loadamberparams ALD.frcmod
> a = loadpdb protein_lig.pdb
> center a
> addions a Cl- 0
> addions a Na+ 0
> solvateoct a d 10 2
> check a
> saveamberparm a SITK04-A-wat.prmtop SITK04-A-wat.inpcrd
> savepdb a SITK04-A-wat.pdb
> quit
> **************
>
>
> The unit "d" is the DMSO box contained in the dmso.off library.
> Apparently, this protocol works fine for small molecules and peptides, but
> when solvating my big protein, a lot of clashes between the solute and
> solvent molecules appear, which preclude proper minimization/equilibration.
> This issue happens more or less irrespective of the "closeness" value I
> specify. I mean, if I specify something like 3 for the closeness, no
> clashes appear, but big holes between the solute and the solvent are
> generated. Strikingly, with something like 2, voids are still observerd,
> but overlapping solvent molecules are still present.
>
> Any clue on how to override this?
>
> Thanks a lot,
>
> Gonzalo
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Thu Jan 05 2012 - 22:00:03 PST
