Hi Dan,
Many thanks for testing this for me.
I should have given more detail as to where the trajectory I used
(test.mdcrd) comes from.
I'm trying to analyze a trajectory produced by NAMD with the CHARMM
force-field, so originally in the .dcd format. I don't have a prmtop for
this system. Instead, I use a pdb file that I created from the original .psf
file.
I first tried reading in the .dcd file, and got the same problems (nan
values for all distance output with multiple atoms in the masks). For
testing, I generated test.mdcrd, with only the first 10 frames from the .dcd
file.
I've now visualized test.mdcrd in VMD, by first reading in the .pdb file I
used for the topology, and then test.mdcrd as "AMBER coordinates" (so
without box info). I don't see any problems in the visualization, i.e. all
atoms positions/bonds look normal.
The puzzling thing for me is that the single atom-atom distance works fine
(either when I read in the .dcd file or the test.mdcrd file), i.e. ptraj
reports the correct distance, whereas any distance with multiple atoms in
one or both of the masks doesn't (i.e. ptraj reports nan).
So, for example, the following both work fine:
distance test1 out test1.dat :82.CA :218.CA
distance test2 out test2.dat :82.N :218.CA
It therefore appears that the coordinates (at least of these three atoms)
are read in and 'understood' correctly by ptraj.
But this gives me "nan" in test3.dat:
distance test3 out test3.dat :82.CA,N :218.CA
I'm happy to send you my test.mdcrd and the pdb I used for the topology
etc., if you would be willing to look into it more.
Many thanks in advance,
Marc
On 19 September 2011 17:44, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I have run ptraj using your input on some trajectories I have here
> (49115 and 4049 atoms, solvated and non-solvated respectively) and
> find no issues. Are you sure that your input trajectory is not corrupt
> (can you visualize it with no problems), and/or that you are using the
> correct topology file?
>
> -Dan
>
> On Mon, Sep 19, 2011 at 5:32 AM, Marc van der Kamp
> <marcvanderkamp.gmail.com> wrote:
> > Hi all,
> >
> > I have a problem with the "distance" command in ptraj. Whenever I give
> masks
> > that specify more than one atom, I get "nan" as the distance in the
> output
> > file. The information in the ptraj log/output indicates that the masks
> > specify the expected number of atoms.
> >
> > Here the input I used for testing:
> >
> > trajin test.mdcrd 1 2 1
> > trajout test2.pdb pdb
> > distance 94-230 out 0_com2.dat :82.CA :218.CA
> > distance 1_COM out 1_com2.dat :36-47.CA :1-217,230-306.CA noimage
> > distance 2_COM out 2_com2.dat :36 .CA noimage
> > distance 3_COM out 3_com2.dat :82 :218
> >
> >
> > Only the first output (0_com2.dat) gives me actual distances, all the
> others
> > all give:
> > 1.00 nan
> > 2.00 nan
> >
> > As mentioned above, the ptraj output doesn't indicate any problem with
> the
> > masks/selections. Relevant snippet from the output follows below.
> > I am using AmberTools 1.5 with all current bugfixes.
> > I must be overlooking something, but I have been trying and testing for a
> > while and can't find out what's going wrong. (And I couldn't find
> anything
> > relevant in the archive.)
> >
> > Thanks in advance for any insights!
> > --Marc
> >
> > ptraj output snippet:
> >
> > PTRAJ: distance 94-230 out 0_com2.dat :82.CA :218.CA
> > Mask [:82.CA] represents 1 atoms
> > Mask [:218.CA] represents 1 atoms
> >
> > PTRAJ: distance 1_COM out 1_com2.dat :36-47.CA :1-217,230-306.CA noimage
> > Mask [:36-47.CA] represents 12 atoms
> > Mask [:1-217,230-306.CA] represents 294 atoms
> >
> > PTRAJ: distance 2_COM out 2_com2.dat :36 .CA noimage
> > Mask [:36] represents 14 atoms
> > Mask [.CA] represents 306 atoms
> >
> > PTRAJ: distance 3_COM out 3_com2.dat :82 :218
> > Mask [:82] represents 15 atoms
> > Mask [:218] represents 14 atoms
> > test.mdcrd: 10 frames.
> >
> > PTRAJ: Successfully read the input file.
> > Coordinate processing will occur on 2 frames.
> > Summary of I/O and actions follows:
> >
> > INPUT COORDINATE FILES
> > File (test.mdcrd) is an AMBER trajectory with 2 sets
> >
> > OUTPUT COORDINATE FILE
> > File (test2.pdb) is a PDB file
> >
> > ACTIONS
> > 1> DISTANCE: between the atoms selections center of mass will be
> > saved to array named 94-230
> > 2> DISTANCE: between the atoms selections center of mass will be
> > saved to array named 1_COM
> > Imaging has been disabled
> > 3> DISTANCE: between the atoms selections center of mass will be
> > saved to array named 2_COM
> > Imaging has been disabled
> > 4> DISTANCE: between the atoms selections center of mass will be
> > saved to array named 3_COM
> >
> >
> > Processing AMBER trajectory file test.mdcrd
> >
> > 100%
> >
> >
> > PTRAJ: Successfully read in 2 sets and processed 2 sets.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Tue Sep 20 2011 - 03:00:02 PDT
