[gmx-users] -ter option with pdb2gmx

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 19 17:43:18 CEST 2011

On 20/08/2011 1:27 AM, Vijayaraj wrote:
> "-ter" or "-inter" options of pdb2gmx are working fine with all force 
> fields except amber force field. I cant select the terminal groups 
> when I use amber ff, it directly goes through the generation of top 
> files without asking any options for terminal group selection. I just 
> want to use the none option for the terminals (with amber ff). any 
> suggestion?

AMBER treats charges on terminal residues differently, so the -ter 
mechanism doesn't work in the way that it can for other force fields. 
See http://ffamber.cnsm.csulb.edu/#usage.

You'd have found this out faster if your earlier email had had a 
one-sentence description of your simulation objective. :)


> Regards,
> Vijay
>     Date: Fri, 19 Aug 2011 15:31:04 +0200
>     From: Vijayaraj <vijayaraj81 at gmail.com <mailto:vijayaraj81 at gmail.com>>
>     Subject: [gmx-users] -ter option with pdb2gmx
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Message-ID:
>     <CAE-dxS-xCLP=pVjgERGKm2yoj0qO=2B7QQQx5p=5Wa=vAJ4BLw at mail.gmail.com <mailto:vAJ4BLw at mail.gmail.com>>
>     Content-Type: text/plain; charset="iso-8859-1"
>     Hello,
>     I am trying to use "-ter" with the pdb2gmx command, seems its not
>     working
>     fine.
>     >pdb2gmx -f <file.pdb> -o <file.gro> -p <file.top> -ter
>     I also used "-inter" option, its not working.
>     I am using 4.5.4 version. any help would be greatly appreciated.
>     Regards,
>     vijay

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