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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Received on Thu Jan 05 2012 - 09:30:03 PST
