Re: Nanotubes with AMBER

From: David Case <>
Date: Sun 11 Aug 2002 21:13:23 -0700

On Sun, Aug 11, 2002, Stefan Andreev Andreev wrote:

> seems that some
> C-C bonds get stretched very far (to 2.86 Angstroms). It seems that the
> 1-2 nearest neighbor VdW interactions don't get excluded in the energy
> calculation, which makes the energy to become huge.

I don't recall seeing any previous error report about corruption of the
non-bonded exclusion list. Make sure that there is in fact a bond between
the two atoms in question. Try putting in a print statement triggered
by a non-bonded interaction between the same two atoms. You can also
examine the exclusion list as it is read in to make sure it seems OK (of
course, it could be getting clobbered later on.)

If this doesn't work, you will have to provide more detailed information.
(Note that Amber does not support periodic calculations in cases where
there are bonds between neighboring unit's not clear from your
brief description whether your nanotubes fit this restriction or not.)

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Sun Aug 11 2002 - 21:13:23 PDT
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