BondDefinition and AnglesDefinition not recognized

Emily Sprague-Klein

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Apr 28, 2020, 5:15:15 AM4/28/20

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Hi Bachir,

I've been running fullrmc under a few different constraint scenarios and realized that as my rather large, messy molecule (>80 atoms) undergoes prolonged stochastic optimization, some of the outer ligands start to fragment (especially the hydrogens and carbons). I've gone back through and checked the I've written the BA, B and IA constraints properly (which seem to be fine), however I noticed the following lines at the beginning of my fullrmc output file that I'm not sure how to fix:

2020-04-26 16:02:01 - fullrmc <INFO> Given constraints will be added to all normal frames in engine

2020-04-26 16:02:01 - fullrmc <USAGE> Molecule name 'Co_cubane_water_create_final' in bondsDefinition is not recognized, bonds definition for this particular molecule is omitted

2020-04-26 16:02:01 - fullrmc <USAGE> Molecule name 'Co_cubane_water_create_final' in anglesDefinition is not recognized, angles definition for this particular molecule is omitted

2020-04-26 16:02:01 - fullrmc <INFO> Saving Engine and frame 0 data... DON'T INTERRUPT

2020-04-26 16:02:04 - fullrmc <INFO> Engine and frame 0 data saved successfuly to '/blues/gpfs/home/spraguea/Co_water_run2_low_r/Co4O4_watershell_engine.rmc'

2020-04-26 16:02:04 - fullrmc <INFO> Running 'atoms' mode step 0

2020-04-26 16:02:04 - fullrmc <INFO> @0 Initializing constraint data 'PairDistributionConstraint'

2020-04-26 16:02:04 - fullrmc <INFO> @0 Initializing constraint data 'BondConstraint'

2020-04-26 16:02:04 - fullrmc <INFO> @0 Initializing constraint data 'BondsAngleConstraint'

2020-04-26 16:02:04 - fullrmc <INFO> @0 Initializing constraint data 'ImproperAngleConstraint'

2020-04-26 16:02:04 - fullrmc <INFO> @0 Initializing constraint data 'InterMolecularDistanceConstraint'

2020-04-26 16:02:04 - fullrmc <INFO> Engine @0 started 59360 steps, total standard error is: 40858.472656

Is fullrmc recognizing my bond and angle definitions? How can I be sure that it's applying my constraints?

Thank you!
Emily

Bachir Aoun

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Apr 28, 2020, 3:38:37 PM4/28/20

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Hi Emily,

Based on the warning message, fullrmc is unable to find the molecule name 'Co_cubane_water_create_final'

which is normal.

A molecule name in fullrmc is nothing else than the residue-name in the pdb file and for fullrmc to recognize molecules you need to make sure that your pdb file is well formatted.

take a look a this

http://bachiraoun.github.io/fullrmc/fullrmc.FAQ.pdbFile.html

If your pdb file is not well formatted, you can specify your bonds and angles using atoms indexes which becomes a bit more laborious to do. I highly recommend you creating a good pdb file to simplify your life.

in the simulation you are currently running i can almost guarantee that fullrmc is not applying your bond constraints.

regards

Emily Sprague-Klein

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Apr 29, 2020, 4:49:12 PM4/29/20

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Thanks!! I double checked all my spacings/column designations and found the issue which was a residue-name mismatch between my .pdb file and what I called the molecule in the bonds and angles definition.

I'm also trying to implement the Improper Angle Constraint, and am getting the following error message:

2020-04-29 15:42:28 - fullrmc <INFO> Given constraints will be added to all normal frames in engine

C:\Users\emily\Anaconda3\lib\site-packages\fullrmc\Core\Collection.py:883: RuntimeWarning: invalid value encountered in true_divide

gr = 1+Gr[:,1]/(-slope*Gr[:,0])

C:/Users/emily/Desktop/Co cubane RMC with bonds and angles with water shell/run.py:56: RuntimeWarning: invalid value encountered in greater

dataWeights[:np.nonzero(gr[:,1]>0)[0][0]] = 0

2020-04-29 15:42:29 - fullrmc <ERROR> angle third items can't be the same

Traceback (most recent call last):

File "<ipython-input-1-5e79fabbc72b>", line 1, in <module>

runfile('C:/Users/emily/Desktop/Co cubane RMC with bonds and angles with water shell/run.py', wdir='C:/Users/emily/Desktop/Co cubane RMC with bonds and angles with water shell')

File "C:\Users\emily\Anaconda3\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 827, in runfile

execfile(filename, namespace)

File "C:\Users\emily\Anaconda3\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 110, in execfile

exec(compile(f.read(), filename, 'exec'), namespace)

File "C:/Users/emily/Desktop/Co cubane RMC with bonds and angles with water shell/run.py", line 287, in <module>

('N00Q','C00T','C017','C010',-15,15)]})

File "C:\Users\emily\Anaconda3\lib\site-packages\fullrmc\Constraints\ImproperAngleConstraints.py", line 460, in create_angles_by_definition

raise Exception(err)

Exception: None

where my constraint definition looks like this:

IA_CONSTRAINT.create_angles_by_definition( anglesDefinition={"UNK": [ ('C00Z','C00S','C019','C018', -15, 15),

('C016','C019','C016','N00P', -15, 15),

('N00P','C00S','C019','C018', -15, 15),

('C013','C01D','C00Y','C00U', -15, 15),

('C01A','C01D','C00Y','C00U', -15, 15),

('N00O','C01D','C00Y','C00U', -15, 15),

('C01H','C01B','C01E','C01F', -15, 15),

('C012','C01B','C01E','C01F',-15, 15),

('N00R','C01B','C01E','C01F',-15, 15),

('C01G','C00T','C017','C010',-15,15),

('C00V','C00T','C017','C010',-15,15),

('N00Q','C00T','C017','C010',-15,15)]})

any ideas what could be going on? Thanks so much

Emily Sprague-Klein

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Apr 29, 2020, 4:56:08 PM4/29/20

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whoops, please disregard my least message, I figured out the typo in the second line.

thanks,
Emily

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