Hello,
I am trying to run a MD of hemoglobin. After preparing all necessary input
with Xleap I minimize the sistem with Sander (four different minimizations)
and everything it is fine. Then I have four stages of equilibration (100 ps
each). These are ran with CUDA version. The simulation dies giving the
following error message:
*Hydrogen atom 219 appears to have multiple bonds to atoms 220 and 221
which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.*
There is a problem: Atom 219 is NOT a hydrogen, is a carbon... So I try to
run normal Sander (no CUDA acceleration) and everything it is fine!
I am using Amber 11 and preparing the system with Amber Tools 12.
Do you have any idea of which could be the problem? Thanks in advance.
Best regards,
Emanuele
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Received on Thu Sep 06 2012 - 02:30:04 PDT
