[AMBER] leap mis-specified improper dihedral

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Tue, 20 Dec 2011 12:23:02 -0600

Dear all,

I am to understand that the improper is specified as (Y-Y-X-Y) on an sp2
hybridized center where X is the sp2 center atom.

When I ran xleap, I obtain an improper that is (Y-X-Y-Y) where all the
atoms are correct, except the sp2 center is in the second position of the
specified dihedral.

Is there a problem here? Will the energies/forces be calculated
correctly? Or am I missing something...

Also, I notice that in a heteroaromatic fused ring system like adenine,
the impropers are only assigned to sp2 centers that have an exocyclic
substituent, and NOT the bridging aromatic sp2 centers.
I have a modified adenine that I am parameterizing and it contains another
fused ring to the pyrimidine portion of adenine, and xleap adds an
improper to a bridging sp2 center on one of the bridging atoms. Is this
simply xleap doing the best it can, or is it a mis-specification?

Of course, I can fit with or without the improper and see if I get a
better SS error, but I was just curious if it is a rule that xleap
"should" not be adding impropers to bridging sp2 aromatic atoms.

Thanks very much in advance for your help!


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Received on Tue Dec 20 2011 - 10:30:04 PST
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