Amber crd file type? Proper format

Zterrano zack.te... at gmail.com
Fri Jun 25 22:12:20 CEST 2010


Sorry, my earlier upload must not have gone through.  The following
files are h2o.tar.gz, TP3NVT.rstrt, and tp3.prmtop.

Zack

On Jun 25, 3:14 pm, Laino Teodoro <teodor... at gmail.com> wrote:
> Sorry my crystal ball is broken.  But unless you share your file with  
> the rest of the people here, you can look into this problem yourself.
>
> Teo
>
> On 25 Jun 2010, at 20:12, Zterrano wrote:
>
>
>
> > Interesting, that is what I expected.  Any idea why the
> > read_atoms_input _parser fails then?
>
> > Zack
>
> > On Jun 25, 12:06 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> >> That's what is implemented (crd/restart which is the same that  
> >> comes out
> >> from leap):
>
> >>http://ambermd.org/formats.html#restart
>
> >> Teo
>
> >> Zterrano wrote:
> >>> I am sure I'm missing something simple here, but I cannot get  
> >>> cp2k to
> >>> read in my coordinates from an Amber restart file.
> >>> I'm curious as to what the authors mean "COORD_FILE_FORMAT CRD"
> >>> because when I try and load a valid .mdcrd or .rstrt file from an
> >>> Amber calculation I get the following error:
> >>> *** 11:39:26 ERRORL2 in cp_parser_methods:parser_get_integer
> >>> processor      ***
> >>> ***   0  err=-300  An integer type object was expected,
> >>> found               ***
> >>> *** <28.9722114>file:'/afs/crc.nd.edu/user/z/zterrano/cp2k/water/
> >>> TP3NVT.cr  ***
> >>> *** ' line:     1 col:    1
> >>> chunk:'28.9722114'                              ***
> >>> The 28.9722114 is the first number in the .mdcrd file.
>
> >>> Why would it be expecting an integer?  All crd files start with the
> >>> coordinates (real numbers).  If I try the .rstrt file which has an
> >>> integer (the total number of atoms present) I get the following  
> >>> error:
> >>> *** 11:49:41 ERRORL2 in atoms_input:read_atoms_input processor
> >>> 0   ***
> >>> *** err=-300  condition FAILED at line
> >>> 120                              ***
>
> >>> Any thoughts?
> >>> Here is my SubSys input:
> >>> &SUBSYS
> >>>   &CELL
> >>>       ABC   19.6207740  19.9210482  19.6524523
> >>>   &END CELL
> >>>   &TOPOLOGY
> >>>       CONN_FILE NAME /cp2k/water/tp3.prmtop
> >>>       CONN_FILE_FORMAT AMBER
> >>>       COORD_FILE_NAME /cp2k/water/TP3NVT.crd
> >>>       COORD_FILE_FORMAT CRD
> >>>  &END TOPOLOGY
> >>>  &COORD
> >>>  &END COORD
> >>>  &END SUBSYS
>
> >>> Thank you in advance!
>
> >>> Zack
>
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