Thanks Dan !
It seems it is the time to switch from ptraj to cpptraj :))
Best wishes,
Marek
Dne Fri, 27 Jul 2012 18:45:41 +0200 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> Hi,
>
> 'lastframe' is only supported by cpptraj.
>
> -Dan
>
> On Fri, Jul 27, 2012 at 10:01 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>> 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/
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Fri Jul 27 2012 - 10:00:02 PDT
