<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>
<br>Regards,<br>Vijay<br><br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Date: Fri, 19 Aug 2011 15:31:04 +0200<br>
From: Vijayaraj <<a href="mailto:vijayaraj81@gmail.com">vijayaraj81@gmail.com</a>><br>
Subject: [gmx-users] -ter option with pdb2gmx<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<CAE-dxS-xCLP=pVjgERGKm2yoj0qO=2B7QQQx5p=5Wa=<a href="mailto:vAJ4BLw@mail.gmail.com">vAJ4BLw@mail.gmail.com</a>><br>
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<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>
</blockquote></div><br></div>