Hello again Daniel,
I followed your instructions and I can now calculate the RMSD and the
mass-weighted RMSD. So far, so good...
Now, there is a notable difference between the values obtained with
calculate_rmsd.py (
https://github.com/charnley/rmsd/tree/master/rmsd)
and QMol (Windows application).
Using both of them I come to the same results:
a) RMSD
01 vs v2 10.901
b) mass-weighted RMSD
01 vs v2 10.874
But when I use cpptraj, the results differ quite a lot:
c) RMSD - cpptraj
01 vs 02 12.5962
d) mass-weighted RMSD - cpptraj
01 vs 02 12.6316
For both cases [a) and b)] the only modification is rotation=none; with
cpptraj, "nofit" does the same.
Still, I do not know why cpptraj's results are so different from the
other tools...
Am I overseeing the obvious?
Thanks and regards,
Martin
On 2020-05-05 23:26, Martin Mielke wrote:
>
> Hi Daniel,
>
> Thanks for your reply.
>
> I will give it a try and, most probably, will write a wrapper script
> that accepts file1.pdb and file2.pdb as arguments...
>
> Also thanks for pointing me in the right direction!
>
>
> Best,
>
> Martin
>
> On 2020-05-05 15:08, Daniel Roe wrote:
>> Hi,
>>
>> On Mon, May 4, 2020 at 9:23 AM Martin Mielke<m_mlk.yahoo.com> wrote:
>>> 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
>> This will require a short input file. Something like a file named e.g.
>> myinput.in:
>>
>> # load reference pdb
>> parm pdb1.pdb
>> reference pdb1.pdb parmindex 0
>> # load target pdb
>> parm pdb2.pdb
>> trajin pdb2.pdb parmindex 1
>> # Calculate RMSD
>> rmsd RMS reference mass
>> run
>> printdata RMS
>>
>> Then run 'cpptraj -i myinput.in'.
>>
>> This will be a best-fit RMSD by default, assumes that pdb1.pdb and
>> pdb2.pdb have the exact same atoms, and that you want the final RMSD
>> to include every atom. If the PDBs are different you would have to
>> give mask expressions that describe the regions you want to use in the
>> RMSD calculation. There needs to be a 1 to 1 correspondence between
>> the atoms in the target and reference structures for the RMSD to be
>> meaningful.
>>
>> Please let me know if you have more questions. It's probably also a
>> good idea to look at the 'rmsd' command section of the cpptraj manual,
>> and maybe do 1 or 2 of the basic cpptraj tutorials
>> (https://ambermd.org/tutorials/TrajectoryAnalysis.php). If you run
>> cpptraj interactively (by just typing cpptraj with no other input) and
>> type 'help rmsd', it will show you the command syntax.
>>
>> Hope this helps,
>>
>> -Dan
>>
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Received on Wed May 06 2020 - 06:30:08 PDT
