VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Oct 19 2016 - 20:14:58 CDT

I don’t have your files, but in all likelihood this is because if you have enough waters, you end up with duplicate chain/residue name combinations. As I noted in my previous reply on the thread, autopsf isn’t designed to handle fully solvated structures. You’ll have to write a manual psfgen script to get this to work well.

> On Oct 19, 2016, at 6:48 PM, 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 ...
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> 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.2013-2014/2214.html
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> 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 ...
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> 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.
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> 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.
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> Is there any solution for this?
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> Thanks
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