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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 05 2020 - 14:30:03 PDT
