Hi,
I get the following error with pmemd.cuda (coming from cuda/gpu.cpp):
1783: 3557 - 3558 and 1785: 3558 - 3559
Hydrogen atom 3558 appears to have multiple bonds to atoms 3557 and
3559 which is illegal for SHAKEH. Exiting due to the presence of
inconsistent SHAKEH hydrogen clusters.
It is unclear to me what is happening here. The first water hydrogen
of the system (index 3558) is bonded to the oxygen (index 3557) and the
other hydrogen (index 3559). ParmEd does not report any other atoms
bonded to index 3558. I do not know what 1783 and 1785 stand for.
The prmtop file is a conversion (parmed chamber) from a CHARMM psf
(using a CHARMM force field generated with CHARMM) file. I have other
such setups which work just fine.
Cheers,
Hannes.
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Received on Mon Sep 26 2016 - 08:00:02 PDT
