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On 20/08/2011 1:27 AM, Vijayaraj wrote:
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<div dir="ltr">"-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?<br>
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<br>
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 <a href="http://ffamber.cnsm.csulb.edu/#usage">http://ffamber.cnsm.csulb.edu/#usage</a>.<br>
<br>
You'd have found this out faster if your earlier email had had a
one-sentence description of your simulation objective. :)<br>
<br>
Mark<br>
<br>
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<br>
Regards,<br>
Vijay<br>
<br>
<br>
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.8ex;border-left:1px #ccc solid;padding-left:1ex;">
Date: Fri, 19 Aug 2011 15:31:04 +0200<br>
From: Vijayaraj <<a moz-do-not-send="true"
href="mailto:vijayaraj81@gmail.com">vijayaraj81@gmail.com</a>><br>
Subject: [gmx-users] -ter option with pdb2gmx<br>
To: <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<CAE-dxS-xCLP=pVjgERGKm2yoj0qO=2B7QQQx5p=5Wa=<a
moz-do-not-send="true"
href="mailto:vAJ4BLw@mail.gmail.com">vAJ4BLw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello,<br>
<br>
I am trying to use "-ter" with the pdb2gmx command, seems
its not working<br>
fine.<br>
<br>
>pdb2gmx -f <file.pdb> -o <file.gro> -p
<file.top> -ter<br>
<br>
I also used "-inter" option, its not working.<br>
I am using 4.5.4 version. any help would be greatly
appreciated.<br>
<br>
Regards,<br>
vijay<br>
<br>
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