[AMBER] Dummy atom and PMEMD

From: Miroslav Krepl <krepl.seznam.cz>
Date: Sun, 05 Oct 2014 22:11:58 +0200

Dear Amber users,

by any chance, did any of you eventually figure out a solution to this
problem:

http://archive.ambermd.org/201208/0452.html

?

I can confirm that two years later, the pmemd.MPI in amber 14 is still
doing the same thing for my dummy atoms, i.e. reporting message

"ERROR: PMEMD does not support single H residues! "

for my dummy atom and then crushing down...

I have been using transformation into dummy atoms in the newly
implemented one-topology Thermodynamic integration in pmemd.

---
I think that I managed to identify the cause of the problem...
I tried changing different parameters of the dummy atoms using parmed.py
and I eventually figured out that the zero atomic mass is somehow
offending the pmemd...
It seems that pmemd thinks all atoms with smaller mass than hydrogen
(e.g. the zero-mass dummy atoms) are hydrogen!!!!
I tried setting the dummy mass to "0"... simulation crushed with the
message.
I tried setting the dummy mass to "1"... simulation crushed with the
message.
I tried setting the dummy mass to "2"... simulation run completely fine
(albeit obviously generating wrong results because the dummy atom now
has non-zero mass).
---
Unless I am missing something else, I'd like to report this behavior
(identifying atoms with lower mass than hydrogen as hydrogens) as
possible bug of the pmemd.
Right now it is limiting the applicability of the new TI implementation
(which is pretty great otherwise).
Thank you and best regards,
Miroslav Krepl
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Received on Sun Oct 05 2014 - 13:30:02 PDT