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 - 03:00:04 PDT
