"-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?
Regards, Vijay Date: Fri, 19 Aug 2011 15:31:04 +0200 > From: Vijayaraj <vijayara...@gmail.com> > Subject: [gmx-users] -ter option with pdb2gmx > To: gmx-users@gromacs.org > Message-ID: > <CAE-dxS-xCLP=pVjgERGKm2yoj0qO=2B7QQQx5p=5Wa=vaj4...@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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