From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Jan 06 2016 - 13:39:14 CST
Hi,
I use CGenFF to parameterize the solvent molecules and then assemble
the systems using PackMol:
http://www.ime.unicamp.br/~martinez/packmol/
As PackMol only eliminates steric clashes, you need to run for some
time to equilibrate the solvent.
Another option would be to equilibrate a box of solvent and then use
the VMD Solvate plugin. Here's an example of using Solvate with a box
of coarse grained Martini water (defined by "martini_water.psf" and
"martini_water.pdb"):
solvate sys.psf sys.pdb -b 4.7 -spsf martini_water.psf -spdb
martini_water.pdb -stop martini_water.top -ws 36.4428 -s W -ks "name
W" -minmax {{-100 -100 -250} {100 100 250}} -o sys_sol
Regards,
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
On Wed, Jan 6, 2016 at 12:17 PM, Deng, Jinxia (Nancy)
<jinxianancy.deng_at_zoetis.com> wrote:
> Happy New Year to all!
>
> Just wonder how or where to access solvate models other than water...
>
> Only hint I have is through http://www.mpibpc.mpg.de/grubmueller/downloads/solvate/index.html as listed in a membrane protein tutotial by NAMD, but the link is not working any more.
>
> Looking forward to any of your advice.
>
> Thanks,
>
> Nancy
>
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