Dear Amber users,
I am solvating an uneven surface with a solvent whose library file is not
existing.I made the solvent library using steps below. When I solvate the
uneven surface with these solvent molecules , they appear to stay in clumps
and this does not randomize even after constant pressure equilibration
because of the uneven surface. On the other hand when I solvate with
existing libary with water using TIP3p box they are good. So can anyone
help me on my steps of creating the solvent library where I need to work.
In the process of making the solvent library I use the following process,
x=loadmol2 x.mol2
x1=copy x
solvatebox x x1 20 2
saveamberparm x x.prmtop x.inpcrd
I use constant pressure run to get to the desired density of the solvent.
I used the last restrt file from my simulation to make the new solvent box
which I upload in xleap to make the solvent library file.
y=loadmol2 x_equil.mol2
setbox y vdw 1
saveoff y y.off
Now I use this y,off to solvate my surface,
Thank you for any suggestions.
Regards
Kirtana
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Received on Thu May 01 2014 - 18:30:02 PDT
