[AMBER] Bond distance and Box shape

From: Arjun Sharma <arjunsharma83.gmail.com>
Date: Fri, 20 Mar 2015 10:21:58 -0400

Dear Amber users,

Iím trying create a cyclic polymer with over 30 monomer units. The first and last units have N-C bond to make it cyclic. In tleap, when I try to bond these two atoms. I get the warning that the bond distance is over 60 A. So basically it is not bonding. This is not the case when I use fewer polymer units (3-4) to make it cyclic. I have created the cyclic polymer with over 30 units before and donít remember coming across this problem. The Polymer Iím trying create now is way heavier compared to the previous one. How do I make these atoms bond?

Another unrelated question, the overall structure of the polymer is cylindrical. Iím trying to force cubic box shape in tleap but it doesnít seem to work. It just gets stuck at the solvatebox step. I did try truncated octahedron and that works just fine. Whatís the issue with cubic box ?


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Received on Fri Mar 20 2015 - 07:30:04 PDT
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