Hi..
  I listed all the zipped files separately as you said.

g_wham  -bins 1000 pull1.pdo.gz pull2.pdo.gz pull3.pdo.gz pull4.pdo.gz
pull5.pdo.gz -temp 298 -o pmf.xvg

I still have the same problem.
  :-)  G  R  O  M  A  C  S  (-:

              GRoups of Organic Molecules in ACtion for Science

                           :-)  VERSION 3.3.1  (-:


     Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
      Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2006, The GROMACS development team,
           check out http://www.gromacs.org for more information.

        This program is free software; you can redistribute it and/or
         modify it under the terms of the GNU General Public License
        as published by the Free Software Foundation; either version 2
            of the License, or (at your option) any later version.

                               :-)  g_wham  (-:

Option     Filename  Type         Description
------------------------------------------------------------
 -o        pmf.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
-------------------------------------------------------
That is the error which I get....
Thank You for your input..
Also if it is not bothering you can you please send me the modified version
of g_wham by David Bostick else I shall check it once again as I couldn't
find it earlier.
Thanks,
SK


On 7/3/07, Lu Lanyuan <[EMAIL PROTECTED]> wrote:

I just zipped alll the *.pdo files seperately and listed them all when
using g_wham. It's like g_wham <options> pull1.pdo.gz pull2.pdo.gz ... In
the old gromacs versions like 3.1.4, the g_wham was broken and I was using
a version modifined by David Bostick. You can search the mailing list for
that information. I'm not sure whether the old problem of g_wham was fixed
in 3.3.1.
Lanyuan Lu


>From: "Sudha Mani Karra" <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
>Subject: Re: [gmx-users] g_wham and PMF problem
>Date: Tue, 3 Jul 2007 10:08:33 -0500
>
>Hi Mark,
>         when I give only one file in the input for g_wham,
>
>g_wham -o pmf.xvg -hist pull1.pdo ,
>
>It asks me to give a series of inputs.The error which I get is
>    :-)  g_wham  (-:
>
>Option     Filename  Type         Description
>------------------------------------------------------------
>  -o        pmf.xvg  Output       xvgr/xmgr file
>-hist pull1.pdo.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    100  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
>
>-------------------------------------------------------
>Program g_wham, VERSION 3.3.1
>Source code file: gmx_wham.c, line: 314
>
>Fatal error:
>You need to specify a series of pdo files as input
>---------------------------------------------------
>
>Appreciate your help.Thanks,
>SK
>
>
>
>
>
>
>
>On 7/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>>
>> > 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
>>
>>_______________________________________________
>>gmx-users mailing list    gmx-users@gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
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>>www interface or send it to [EMAIL PROTECTED]
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>>


>_______________________________________________
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