From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Oct 19 2016 - 14:25:49 CDT

When you say that it is getting held, is there any output going to the console? Do you have an hourglass/spinning lollipop/busy indicator for your mouse cursor when vmd is active? How long have you waited?
The ideal workflow is to run autopsf and THEN run solvate. Autopsf will take a LONG time on a solvated system because it has to run chain splitting on all of the waters…

Best,
Peter

> On Oct 19, 2016, at 12:13 PM, Life Sciences Inc <contact.lifesciences.inc_at_gmail.com> wrote:
>
> HI ALL
>
> I am trying to create a psf file and pdb file from autopsf , I am addding the charmm 36 force field for lipid and water molecules through topology file "top_all36_lipid.rtf". First I did solvation using Solvate tool of vmd and then I am loading the pdb file from solvate tool to be used in autopsf tool.
>
> Autopsf is making chains and everything is normal, but when the processing comes to the last chains of TIP3 water molecules somehow the tool is getting held and showing no error. I am using VMD 1.9.2 version.
>
> Is there any solution for this?
>
> Thanks
>
>
>