[AMBER] ff19SB with end-caps pmemd.cuda problem

From: Pavlína Pokorná <pokorna.pavlina.ibp.cz>
Date: Wed, 11 Dec 2019 11:37:55 +0100

Dear all,

when attempting simulations with ff19SB with the updated Amber18 version
from Carlos Simmerling's GitHub, I failed to run pmemd.cuda simulations
with ACE and NHE caps on N- and C- termini of the protein. Simulations
crashed with the following error in ~50 nanoseconds: "Error: an illegal
memory access was encountered launching kernel kNLSkinTest". No further
error message is printed in the simulation *.out file and the last-saved
structure showed no abnormalities. Simulations with the same system without
the end-caps run without any problems. Runs with the end-caps with sander
on CPUs do not result in this error. Test ff14SB cuda simulations with the
end-caps with the updated Amber18 run also without problems. I have ~1100
atoms in my system.

It seems that cuda + ff19SB + caps combination produces some large numbers
somewhere. Is there something I am missing or could you advise any possible
solution to my problem?

The ff19SB improved some local backbone conformations (and associated
protein-protein interactions) wrt ff14SB in my protein-protein complex, so
I'd like to use this force field. Still, I need to use the end-caps due to
the excessive and undesired end-end interactions in the structure.

I'd be grateful for any comment.

Best wishes,

Pavlina Pokorna
*PhD student*
Institute of Biophysics of the CAS, v. v. i.
Kralovopolska 135, 612 65 Brno
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Received on Wed Dec 11 2019 - 03:00:01 PST
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