[AMBER] acpype fails to run on provided tests

From: Daniel Bork <dbork.g.hmc.edu>
Date: Mon, 29 Jun 2015 16:27:14 -0400


I have been attempting to use acypye to aid in the generation of topology
files for custom (in this case, N-glycosylated) amino acid residues.
However, it seems to fail to run on 2/4 of the tests provided by the
developers (namely FFF.pdb and KKK.pdb), due to problems with sqm
convergence. Specifically, the error acpype throws is

Error: cannot run "[directory]/amber14/bin/sqm -O -i sqm.in -o sqm.out" of
bcc() in charge.c properly, exit

which presumably results from the sqm error

QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1184E+07 DeltaE = 0.1163E-09 DeltaP = 0.2354E-13
QMMM: Smallest DeltaE = 0.1739E-10 DeltaP = 0.1546E-06 Step = 5

I understand that the listed value for E is quite high; however, this
result occurred even after extensive minimization of the provided
phenylalanine tripeptide, so it is not obvious to me what problems the
initial structure might have. Additionally, on my coworker's computer, this
test successfully runs (after taking a much longer time than sqm took to
announce failure to converge on my machine), so perhaps this could be
partially a hardware issue. In case it is, I am running the latest Ubuntu
release, 14.04.

Thank you so much for your time and any advice you may be able to provide.

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Received on Mon Jun 29 2015 - 13:30:02 PDT
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