VMD-L Mailing List
From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Oct 19 2016 - 17:12:33 CDT
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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
:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/2214.html
On Oct 20, 2016 05:51, "Life Sciences Inc" <
contact.lifesciences.inc_at_gmail.com> wrote:
> 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
>> 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
>>
>>
>>
>>
>
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