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. :)
Mark
Regards,
Vijay
Date: Fri, 19 Aug 2011 15:31:04 +0200
From: Vijayaraj <[email protected] <mailto:[email protected]>>
Subject: [gmx-users] -ter option with pdb2gmx
To: [email protected] <mailto:[email protected]>
Message-ID:
<CAE-dxS-xCLP=pVjgERGKm2yoj0qO=2B7QQQx5p=5Wa=vaj4...@mail.gmail.com
<mailto:[email protected]>>
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
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
