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 <[EMAIL PROTECTED]> 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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