VMD-L Mailing List
From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Mon Oct 22 2012 - 06:15:49 CDT
- Next message: John Stone: "Re: calculate end-to-end distance with trajectory files"
- Previous message: Axel Kohlmeyer: "Re: Re: how to make separate molecule whole?"
- In reply to: Jose Borreguero: "VMD (and NAMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags)"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
load prmtop as Amber7 Parm and mdcrd as Amber7 Restart file type.
On 20 October 2012 23:57, Jose Borreguero <borreguero_at_gmail.com> wrote:
> Dear VMD users,
>
> I generated a simple water box AmberTools 1.5. When VMD1.9 loads the
> prmtop and mdcrd, it shows a system with very very wrong bond
> connectivities. In addition, NAMD2.8 fails when reading the topology file
> but the error message is not informative.
>
> Any help would be immensely appreciated. If you want to try these files
> for yourself in your VMD, here is the link for the prmtop and mdcrd files
> (72Kb)
> http://www.adrive.com/public/XVwBec/files.tar.gz
>
> Best regards,
> Jose M. Borreguero
>
>
>
-- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang_at_pharm.uoa.gr tevang3_at_gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
- Next message: John Stone: "Re: calculate end-to-end distance with trajectory files"
- Previous message: Axel Kohlmeyer: "Re: Re: how to make separate molecule whole?"
- In reply to: Jose Borreguero: "VMD (and NAMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags)"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]