Hi,
Can you provide me off-list the two PDB files in question? That will be the
easiest way for me to figure out what’s going on.
-Dan
On Wed, May 6, 2020 at 9:28 AM Martin Mielke <m_mlk.yahoo.com> wrote:
> 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
> >>
> >> _______________________________________________
> >> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 06 2020 - 07:00:03 PDT
