[AMBER] TI problem

From: Fabrício Bracht <bracht.iq.ufrj.br>
Date: Thu, 11 Oct 2012 15:15:04 -0300

I am trying to run a TI simulation, mutating a zinc bound water
molecule (H-O-H) into a hydroxyl group (O-H). I have set up the
simulation by following the instructions on the amber tutorial A9.
Once I set the two parameter files for the HOH and the OH groups and
run the mpirun -np $NP sander.MPI -O -ng 2 groupfile I get the
following error.

SANDER BOMB in subroutine setup_sc
 All non-softcore atoms must be identical in both systems

Well, the number of atoms of both systems is exactly the same. But the
atoms themselves are not exactly equal, since the system with the HOH
group has "n" charge and the OH has "n-1". Being so, one system has
"n" sodium atoms and the other has "n-1" (so that the system charge
remains 0). The number of water molecules in both systems are the same
and the rest of the protein (non softcore part of the protein) is also
identical. Knowing this, how am I supposed to make both system's
non-softcore atoms identical?

Thank you

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Received on Thu Oct 11 2012 - 11:30:05 PDT
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