VMD-L Mailing List

From: Raviteja Kurapati (tsii.ravi_at_gmail.com)
Date: Wed Nov 16 2016 - 06:18:33 CST

Hi,
I wish to use a spce water model with opls foce field for my simulation.

I am using modified tip3p pdb file (which comes with vmd) to generate psf
from str file provided at http://mackerell.umaryland.edu/charmm_ff.shtml in
c32b1 zip.

When I solvate using this newly made pdb-psf, the total no of water
molecules shows to be 9261 irrespective of box dimensions i put in solvate
plugin or tcl script.

Also I found it impossible to use autoionize plugin to balance the charge
when I name the residue SPCE instead of TIP3.

I also read that it is possible to mention water model used in conf file.
Can you please let me know how.

Thanks,
Raviteja