[AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model

From: Sadegh Faramarzi Ganjabad <safaramarziganjabad.mix.wvu.edu>
Date: Mon, 21 May 2018 14:24:52 -0400


I have converted CHARMM inputs to AMBER inputs. Not sure why but there are
extra bonds between two hydrogen atoms in the water molecules in the
original CHARMM files. When I try to run the AMBER inputs it complains
about those extra bonds. Here is the error I get

 Hydrogen atom 23639 appears to have multiple bonds to atoms 23638 and
23640 which is illegal for SHAKEH.

Is there a way to fix the error? I cannot manually remove all extra bonds
from the original CHARMM inputs, so I was thinking of a way to have AMBER
ignore them.

Sadegh Faramarzi,
Research Assistant
West Virginia University, Department of Chemistry
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Received on Mon May 21 2018 - 11:30:03 PDT
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