Hi Jason,
I found *lhs_f, rhs_f, lhs_g and rhs_g* in the nab-entropy outputs
(attached as tgz files). I could not found the same "terms" in the amber
manuals (Amber11 and AT1.4; by the way, it should be related to xmin of
nab, I guess?? but the two lines in the outputs are missing in the
example scripts of the manual pg 289).
As a second point: *entropy calculation on a large system* (454 res) -
running out of memory on the machines!
How can I increase the memory for the machine (I worked on a 32cpu with
32GB ram also, same result)? Or is it possible, or more likely correct,
isolate one region of the complex to be used for free energy
calculations? Any suggestions on how to do it? (creating a new prmtop
for "extended"
- binding site-inhibitor / strip trajectories from the "BIG" all-atom
traj, and then calculate free energy?
Best regards,
Matthias
l 17.08.2010 14:47, Jason Swails ha scritto:Hello Matthias,
On Tue, Aug 17, 2010 at 4:13 AM, Matthias Negri
<m.negri.mx.uni-saarland.de <mailto:m.negri.mx.uni-saarland.de>> wrote:
Hello Jason,
we experienced some problems in calculating the entropy contribution
for a CYP-inhibitor complex.
We tried several possibilities (nmode, mmpbsa_entropy.nab), but the
only one working was the one where entropy=1 was used (thus,
calculating the entropy via covariant matrix, etc).
However, when we check the single runs for receptor and complex we
always get a "convergence satisfied", but in the MMPBSA.py.MPI
output we got the message that entropy could not be calculated due
to some snapshots not being minimized (which should not be true
because when we minimized the snapshots singularly all of them
reached the requested convergence).
Yes, this error message does need to be changed. What it really means
is that no "Thermochemistry" data was found, but when we used to use
nmode this almost always meant that minimizations were not good enough.
However, with the nab program this is generally no longer the case. I
can't say for certain what the problem is without seeing the stderr
output, but I have my suspicions. Your system is quite large: 454
residues according to your output file. A system of this size will
require considerable memory for an nmode calculation. My guess is that
you were running out of memory on the machines you were running on
(that's the current most popular reason for getting that error message).
Check stderr for indications that you ran out of memory: i.e. segfaults
and the like.
Hope this helps,
Jason
The only output where we can find entropy values is for the ligand,
while for receptor and complex the output file ended with the string
saying convergence satisfied, but when it should start adding the
"iter Total bad vdW elect nonpolar genBorn
frms"
no output was found.
Attached you can find a zipped file including the outputs of the
calculation, and I hope you can give us some useful suggestions on
how to solve this issue.
Let me know if you need other input files. Anyway, enthalpy
calculations run fine, thus I think that the error should not be
linked to the prmtops or the crd files.
Best regards,
Matthias
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Received on Tue Aug 17 2010 - 16:00:03 PDT
