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.
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Received on Mon Sep 19 2011 - 10:00:03 PDT
