VMD-L Mailing List
From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Oct 19 2016 - 17:12:33 CDT
As of charmm36 almost all the things have been defined in seperate files.
What this means is that you don't have water (as tip3p) defined in the
lipid rtf file. You need a seperate file with the tip3p topology. The NAMD
friendly version of this and some discussion around this can be found here
On Oct 20, 2016 05:51, "Life Sciences Inc" <
> Or if anyone can give me simple commands to do process through command
> line ...
> On Wed, Oct 19, 2016 at 6:13 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
>> 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?