[gmx-users] g_wham and PMF problem

[Sudha Mani Karra]

Hey Arneh,
          I did the same way as you told me to do so.
I collected all my *.pdo files into one directory and then using gzip *.pdo
,zipped those files.
Then I used the command line as
g_wham *.gz -bins 1500 -temp 298 -o pmf.xvg
 I still get the same error which is as follows:

  :-)  g_wham  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -o    profile.xvg  Output       xvgr/xmgr file
-hist     histo.xvg  Output       xvgr/xmgr file

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
       -nice    int      0  Set the nicelevel
      -[no]w   bool     no  View output xvg, xpm, eps and pdb files
   -[no]xvgr   bool    yes  Add specific codes (legends etc.) in the output
                            xvg files for the xmgrace program
        -min   real      0  Minimum coordinate in profile
        -max   real      0  Maximum coordinate in profile
       -bins    int   1000  Number of bins in profile
   -[no]prof   bool    yes  Only calculate min and max
       -temp   real    298  Temperature
   -[no]flip   bool     no  Combine halves of profile
        -tol   real   0.01  Tolerance

Opening file pull1.pdo.gz.
-------------------------------------------------------
Program g_wham, VERSION 3.3.1
Source code file: gmx_wham.c, line: 90

Fatal error:
This does not appear to be a valid pdo file



Can you please let me know how to handle this???
Appreciate your help.

Thanks,
SK

-------------------------------------------------------




On 7/3/07, Arneh Babakhani <ababakha at mccammon.ucsd.edu> wrote:
>
> You have to collect all of the pdo files into one directory (and so you'll
> have to rename them if they all have identical names).  Then zip them
> using gzip: gzip *.pdo
>
> Then you can use the g_wham code, something like:
> g_wham *.gz -bins 1000 -temp 300 -auto
>
>
>
> >> Hey Mark,
> >>           Appreciate your immediate response.You can find the input and
> >> the
> >> error below:
> >> g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo
> >> pull5.pdo
> >
> > g_wham -h suggests that -hist won't accept multiple input files. Only a
> > few GROMACS utilities will do magic concatenation for you. Have a look
> at
> > the file format and see what you need to do with a text editor or
> command
> > line tools.
> >
> >> Opening file pull2.pdo.
> >>
> >> gunzip: stdin: not in gzip format
> >> -------------------------------------------------------
> >> Program g_wham, VERSION 3.3.1
> >> Source code file: gmx_wham.c, line: 90
> >>
> >> Fatal error:
> >> This does not appear to be a valid pdo file
> >> -------------------------------------------------------
> >
> > Does g_wham -o pmf.xvg -hist pull1.pdo work?
> >
> > Mark
> >
> > _______________________________________________
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