AMBER Archive (2009)

Subject: Re: [AMBER] New atom type with 7 bonds

From: David A. Case (
Date: Mon Feb 16 2009 - 08:28:25 CST

On Fri, Feb 13, 2009, Akansha Saxena wrote:
> I am building a new molecule in my simulations with 2 new atom
> types: XZ and DX. The molecule consists of 1XZ and 7 DXs i.e. 8 atoms
> where XZ is bonded to the remaining 7 atoms. When I build the molecule
> in XLEAP and draw bonds between the atoms, the software does not let me
> connect XZ to anything more than 6. Is there a limit in XLEAP on the
> number of bonds I define for an atom?

There is a MAXBONDS parameter in $AMBERHOME/src/leap/src/leap/atom.h.

In Amber9 and earlier this was set to six, and it is 8 in Amber10. You
could check your value and increase it if you want, then re-compile.
I'm not sure if that affects the visual drawing of bonds in xleap, but
it's is sure worth a try.


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