Re: [AMBER] Bond distance and Box shape

From: Daniel Roe <>
Date: Fri, 20 Mar 2015 08:34:53 -0600


On Fri, Mar 20, 2015 at 8:21 AM, Arjun Sharma <> wrote:
> I’m 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 don’t remember coming across this problem. The Polymer I’m trying create now is way heavier compared to the previous one. How do I make these atoms bond?

My guess is that tleap is building everything linearly, which is why
the distance is so great when you add that bond. Rest assured that
when you add a bond in tleap it is there (even if it's 60 Ang long),
it's just far from equilibrium. You could try careful minimization of
that structure but my feeling is that you will get better results if
you do some structure manipulation as you are building the monomer,
via e.g. the 'impose' command. You could even try building small
segments and using distance restraints to slightly "bend" the pieces
before loading them back into leap and adding on another few units.

> Another unrelated question, the overall structure of the polymer is cylindrical. I’m trying to force cubic box shape in tleap but it doesn’t seem to work. It just gets stuck at the solvatebox step. I did try truncated octahedron and that works just fine. What’s the issue with cubic box ?

You need to provide the exact input you tried with leap and the exact
output it gave you.


> Thanks,
> Ashar
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 20 2015 - 08:00:02 PDT
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