Hello all,
it seems that ptraj in Amber12 ignores (is not able to process) trajin
parameter "lastframe"
at least in my case :))
This warning:
"WARNING in getArgumentInteger(): Scanning integer argument failed"
suggests that ptraj expects some number instead the keyword "lastframe"
although in AmberTools12 manual is e.g. written:
--------------------------------------------
To explicitly select only the last frame, specify the lastframe keyword:
trajin Test1.crd lastframe
----------------------------------------
So ???
Any comments welcomed !
Best wishes,
Marek
Problem definition:
#1 My ptraj input file (prod_REIMAGED.mdcrd is in netcdf format and the
box is octahedric)
-------------------------------------------------------------------------------------------
trajin prod_REIMAGED.mdcrd lastframe
radial WATER.RDF 0.5 5.0
:WAT :CEN.N1
-------------------------------------------------------------------------------------------
#2 Relevant part of of the ptraj info output
---------------------------------------------------------------------------------------------
Setting box to be an exact truncated octahedron, angle is 109.471221
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin prod_REIMAGED.mdcrd lastframe
Checking coordinates: prod_REIMAGED.mdcrd
NETCDF file:
WARNING in getArgumentInteger(): Scanning integer argument failed
PTRAJ: radial WATER.RDF 0.5 5.0
:WAT :CEN.N1
Mask [:WAT] represents 88143 atoms
Mask [:CEN.N1] represents 1 atoms
[No output trajectory specified (trajout)]
prod_REIMAGED.mdcrd: 200 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 (prod_REIMAGED.mdcrd) is a NetCDF AMBER trajectory with box info
with 200 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> RADIAL DISTRIBUTION FUNCTION: Output to WATER.RDF
spacing is 0.500
maximum is 5.000
[This implies 10 bins]
density is 0.033
RDF will bin all solute-mask to solvent-mask distances
Solvent atom selection is :382-29762
Solute atom selection is :1.N1
-----------------------------------------------------------------------------------------------------
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 27 2012 - 09:30:03 PDT
