Dear David,
The QM region consists of 22 heavy atoms and 21 hydrogens.
The job has been running all day and has produced a 1.2GB data file, which is nearly entirely filled with the given errors. I will do as you suggest.
The `checkstructure` command:
> parm protein.prmtop
> trajin heat.rst
> checkstructure
> run
was done on the heating (previous stage) coordinates and the output shows no errors, I assume...:
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: BlaC.prmtop, 45184 atoms, 10568 res, box: Orthorhombic, 10304 mol, 10294 solvent
INPUT TRAJECTORIES (1 total):
0: 'heat.rst' is a NetCDF AMBER restart file with coordinates, velocities, time, box, Parm BlaC.prmtop (Orthorhombic box) (reading 1 of 1)
Coordinate processing will occur on 1 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'BlaC.prmtop' (1 actions):
0: [checkstructure]
Using pair list.
Total Grid memory: 240.592 MB
TIME: Pair List Setup: 0.3338 s
Grid dimensions: 53 55 57 (166155 total).
Excluding bond interactions.
Memory used by full exclusion list: 542.464 kB
Mask [*] corresponds to 45184 atoms.
Checking 45216 bonds.
Imaging on.
----- heat.rst (1-1, 1) -----
100% Complete.
Read 1 frames and processed 1 frames.
TIME: Avg. throughput= 2.1715 frames / second.
ACTION OUTPUT:
TIME: Analyses took 0.0000 seconds.
DATASETS (1 total):
CHECK_00001 "CHECK_00001" (integer), size is 1 (0.004 kB)
Total data set memory usage is at least 0.004 kB
DATAFILES (1 total):
STDOUT (Structure check)
RUN TIMING:
TIME: Init : 0.0000 s ( 0.01%)
TIME: Trajectory Process : 0.4605 s ( 91.65%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.01%)
TIME: Other : 0.0419 s ( 0.08%)
TIME: Run Total 0.5024 s
---------- RUN END ---------------------------------------------------
Best,
--
Maciej Spiegel, MPharm
Department of Pharmacognosy and Herbal Medicines
Wroclaw Medical University
https://farmaceut.github.io <https://farmaceut.github.io/>
.ORCiD <https://orcid.org/0000-0002-8012-1026> @Publons <https://publons.com/researcher/4419515/maciej-spiegel/>
Reviewer at:
Phytochemistry | Free Radical Research | Theoretical Chemistry Accounts
Journal of Molecular Modeling | Frontiers in Bioscience-Landmark | Symmetry
> Wiadomość napisana przez David A Case <david.case.rutgers.edu> w dniu 20.02.2023, o godz. 14:56:
>
> On Sun, Feb 19, 2023, Maciej Spiegel via AMBER wrote:
>
>> I run QM/MM computation but the QM region does not converge at all, and
>> Amber keeps throwing errors:
>
> How many atoms are in your QM region? Larger regions increase the chances
> of SCF failures.
>
> Try running just enough steps to get to a failure, and look at the
> coordinates in the restart file. See if the "checkstructure" action in
> cpptraj reports any problems.
>
> ...good luck...dac
>
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Received on Mon Feb 20 2023 - 05:30:02 PST
