Dear all,
I trust this message will find you well.
I am new to AmberTools so please bear with me if this has already been
discussed here. I searched before sending message but I could not find a
straight answer...
There is a Python script which can be used to calculate the RMSD and it
can be found here
https://github.com/charnley/rmsd/tree/master/rmsd if you are curious.
There is another Windows tool called QMol which also calculates the RMSD.
These are the options I get in my current (latest) calculate_rmsd.py:
---] START OF PASTED TEXT
martin.rigel:~> calculate_rmsd -v
rmsd 1.3.2
See
https://github.com/charnley/rmsd for citation information
martin.rigel:~> calculate_rmsd
usage: calculate_rmsd [options] FILE_A FILE_B
Calculate Root-mean-square deviation (RMSD) between structure A and B,
in XYZ
or PDB format, using transformation and rotation.
For more information, usage, example and citation read more at
https://github.com/charnley/rmsd
positional arguments:
FILE_A structures in .xyz or .pdb format
FILE_B
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-r METHOD, --rotation METHOD
select rotation method. "kabsch" (default),
"quaternion" or "none"
-e, --reorder align the atoms of molecules (default: Hungarian)
--reorder-method METHOD
select which reorder method to use; hungarian
(default), brute, distance
--use-reflections scan through reflections in planes (eg Y
transformed to -Y -> X, -Y, Z) and axis changes, (eg
X and Z coords exchanged -> Z, Y, X). This will
affect stereo-chemistry.
--use-reflections-keep-stereo
scan through reflections in planes (eg Y
transformed to -Y -> X, -Y, Z) and axis changes, (eg
X and Z coords exchanged -> Z, Y, X).
Stereo-chemistry will be kept.
-nh, --no-hydrogen ignore hydrogens when calculating RMSD
--remove-idx IDX [IDX ...]
index list of atoms NOT to consider
--add-idx IDX [IDX ...]
index list of atoms to consider
--format FMT format of input files. valid format are xyz and pdb
-p, --output, --print
print out structure B, centered and rotated unto
structure A's coordinates in XYZ format
martin.rigel:~>
---] END OF PASTED TEXT
There is an option in QMol to also calculate a mass-weighted RMSD which,
as of this writing, it is not yet present in the Python script mentioned
above.
Because the main idea is to batch-process several PDB files, a script is
preferred over a Windows application.
Compared to QMol, it seems like enabling/disabling such an option it
yields different results.
For example:
Both with calculate_rmsd 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
With QMol and "mass weighting" enabled:
01 vs v2 10.874 <--- different
v1 vs v3 0.179
v1 vs v4 5.933<--- different
v1 vs v5 10.902 <--- different
A few Google searches later, I found AmberTools, pytraj and, later, its
improved version cpptraj.
It seems like calculating a mass-weighted RMSD is possible too, so I was
wondering if someone would point me to the right direction in telling me
how to use cpptraj in a way that it yields the mass-weighted RMSD for 2
given PDB files? All I want is the final value shown on screen, no graph
files etc needed.
For example:
$ cpptraj [options for mass-weighted RMSD here] file1.pdb file2.pdb [hit
enter]
10.874
Thank you very much in advance!
Please stay safe and healthy!
Best Regards,
Martin
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Received on Mon May 04 2020 - 06:30:04 PDT
