[gmx-users] -ter option with pdb2gmx

Vijayaraj vijayaraj81 at gmail.com
Fri Aug 19 17:27:16 CEST 2011

"-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?


Date: Fri, 19 Aug 2011 15:31:04 +0200
> From: Vijayaraj <vijayaraj81 at gmail.com>
> Subject: [gmx-users] -ter option with pdb2gmx
> To: gmx-users at gromacs.org
> Message-ID:
>        <CAE-dxS-xCLP=pVjgERGKm2yoj0qO=2B7QQQx5p=5Wa=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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