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Hi all!
I trust you guys are all safe and healthy during this COVID-19 pandemic.
Quick question: is there any way to calculate the RMSD contemplating the mass-weighting? If not, would someone be willing to add it? :-)
Please see http://archive.ambermd.org/200805/0482.html for further info.
Compared to, for example, QMol, it seems like enabling/disabling such an option yields different results.
For example: Results from calculate_rmsd.py and QMol with "mass weighting" disabled: 01 vs v2 10.902 v1 vs v3 0.179 v1 vs v4 5.950 v1 vs v5 10.929
They are identical.
Now with QMol and "mass weighting" enabled: 01 vs v2 10.874 v1 vs v3 0.179 v1 vs v4 5.933 v1 vs v5 10.902
As you can appreciate, there is a slight difference but it makes a rather huge change...
QMol's source-code can be downloaded here: http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml
I only found references to "mass weight" in QMol's kabsch.cpp and kabsch.h
I know that there is a weighted Kabsch algorithm (thanks Jimmy for the info) https://github.com/charnley/rmsd/blob/master/rmsd/calculate_rmsd.py#L229
but, from what I see in the calculate_rmsd.py options, there are no ways to call that function.
Volunteers? :-)
Thanks a lot in advance for your time and consideration!
I look forward to hearing from you soon!
Please stay safe!
Best, Martin
The text was updated successfully, but these errors were encountered:
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Hi all!
I trust you guys are all safe and healthy during this COVID-19 pandemic.
Quick question: is there any way to calculate the RMSD contemplating the mass-weighting? If not, would someone be willing to add it? :-)
Please see http://archive.ambermd.org/200805/0482.html for further info.
Compared to, for example, QMol, it seems like enabling/disabling such an option yields different results.
For example:
Results from calculate_rmsd.py and QMol with "mass weighting" disabled:
01 vs v2 10.902
v1 vs v3 0.179
v1 vs v4 5.950
v1 vs v5 10.929
They are identical.
Now with QMol and "mass weighting" enabled:
01 vs v2 10.874
v1 vs v3 0.179
v1 vs v4 5.933
v1 vs v5 10.902
As you can appreciate, there is a slight difference but it makes a rather huge change...
QMol's source-code can be downloaded here:
http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml
I only found references to "mass weight" in QMol's kabsch.cpp and kabsch.h
I know that there is a weighted Kabsch algorithm (thanks Jimmy for the info)
https://github.com/charnley/rmsd/blob/master/rmsd/calculate_rmsd.py#L229
but, from what I see in the calculate_rmsd.py options, there are no ways to call that function.
Volunteers? :-)
Thanks a lot in advance for your time and consideration!
I look forward to hearing from you soon!
Please stay safe!
Best,
Martin
The text was updated successfully, but these errors were encountered: