Dear All,
I am trying to keep the 10 closest waters around a ligand in a DNA-ligand trajectory.
The ptraj script I am using is:
------------------------------------------------------
trajin md_reimaged.mdcrd 201 400
trajout closest_waters.mdcrd
strip :Na+
closest 10 :13 oxygen
-----------------------------------------------------
The output processing when the script is running looks like below:
-----------------------------------------------------------------------------------------------------------------
PTRAJ: trajin md_reimaged.mdcrd 201 400
Checking coordinates: md_reimaged.mdcrd
Rank: 0 Atoms: 10869 FrameSize: 264142 TitleSize: 30 NumBox: 3 Seekable 1
PTRAJ: trajout closest_waters.mdcrd
PTRAJ: strip :Na+
Mask [:Na+] represents 8 atoms
PTRAJ: closest 10 :13 oxygen
Mask [:13] represents 80 atoms
md_reimaged.mdcrd: 20000 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 200 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (md_reimaged.mdcrd) is an AMBER trajectory (with box info) with 400 sets (processing only 200)
OUTPUT COORDINATE FILE
File (closest_waters.mdcrd) is an AMBER trajectory (with box info)
ACTIONS
1> STRIP: 8 atoms will be removed from trajectory: :14-21
2> CLOSESTWATERS: saving the 10 closest solvent molecules around atoms :13
The current solvent mask is :14-3480
Processing AMBER trajectory file md_reimaged.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
PTRAJ: Successfully read in 200 sets and processed 200 sets.
Dumping accumulated results (if any)
----------------------------------------------------------------------------------------------------------------------------------
The input md_reimaged.mdcrd file was prepared by ptraj with the following script:
--------------------------------------------
trajin md*.mdcrd
trajout md_reimaged.mdcrd
center :1-13
image familiar
go
--------------------------------------------
To execute ptraj I used the following command: ptraj <prmtop filename> <ptraj script filename>
I have also tried noimage, closestwaters, different trajout filenames, not stripping the Na+ ions, and using varying number of trajin frames. However, this does not give a trajectory file I can view using VMD. I am able to view the original md_reimaged.mdcrd file and others like it but not this ptraj processed for closest waters. One strange thing that is happening is that VMD is automatically suggesting it is a pdb file for some reason? Could it be from the order of the lines in the ptraj script or how the md_reimaged.mdcrd file was created?
Kind regards,
Andre
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 04 2012 - 03:00:03 PDT
