[AMBER] TI problem - Antechamber changes the atom order

From: FCUP <Sílvia>
Date: Tue, 15 Feb 2011 11:27:31 +0000

Hello AMBER forum!

I am trying to perform some TI calculations but i encounter a strange

when i am doing the transformation Benzothiophene-->Benzothiophene-5-ol,
occurs a mismatch error.
However this problem only occurs in Benzothiophene-->Benzothiophene-5-ol and
Benzothiophene-->Benzothiophene-7-ol, not appearing in
Benzothiophene-->Benzothiophene-2-ol, Benzothiophene-->Benzothiophene-4-ol
or Benzothiophene-->Benzothiophene-6-ol.
I checked the input files and found that Antechamber changes the atom order
in the alcool inpcrd files of the two first transformations... but i can't
understand why it happends only in this two cases.

Every input file was originated in the same way.

What could be the problem?

Thanks, already, for your help.

Slvia Alexandra Pinto Martins
PhD student
Chemistry Department
Faculty of Sciences
University of Porto
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Received on Tue Feb 15 2011 - 03:30:03 PST
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