VMD-L Mailing List

From: Life Sciences Inc (contact.lifesciences.inc_at_gmail.com)
Date: Wed Oct 19 2016 - 17:48:27 CDT

Yes psf and pdb are made now with autopsf after adding charmm36 lipid
topology file (.rtf) and water_ions.str file, but the new pdb and psf file
does not have many water molecules , autopsf has deleted many of them ...

On Thu, Oct 20, 2016 at 12:46 AM, Life Sciences Inc <
contact.lifesciences.inc_at_gmail.com> wrote:

> Yes psf and pdb are made now with autopsf after adding charmm36 lipid
> topology file (.rtf) and water_ions.str file, but the new pdb and psf file
> does not have many water molecules , autopsf has deleted many of them ...
>
> On Thu, Oct 20, 2016 at 12:12 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> 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.201
>> 3-2014/2214.html
>>
>> On Oct 20, 2016 05:51, "Life Sciences Inc" <contact.lifesciences.inc_at_gmai
>> l.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
>>>>
>>>>
>>>>
>>>>
>>>
>