Hey Arneh,<br> I did the same way as you told me to do so.<br>I collected all my *.pdo files into one directory and then using gzip *.pdo ,zipped those files.<br>Then I used the command line as<br>g_wham *.gz -bins 1500 -temp 298 -o
pmf.xvg<br> I still get the same error which is as follows:<br> <br> :-) g_wham (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br>
-o profile.xvg Output xvgr/xmgr file<br>-hist histo.xvg Output xvgr/xmgr file<br><br> Option Type Value Description<br>------------------------------------------------------<br> -[no]h bool no Print help info and quit
<br> -nice int 0 Set the nicelevel<br> -[no]w bool no View output xvg, xpm, eps and pdb files<br> -[no]xvgr bool yes Add specific codes (legends etc.) in the output<br> xvg files for the xmgrace program
<br> -min real 0 Minimum coordinate in profile<br> -max real 0 Maximum coordinate in profile<br> -bins int 1000 Number of bins in profile<br> -[no]prof bool yes Only calculate min and max
<br> -temp real 298 Temperature<br> -[no]flip bool no Combine halves of profile<br> -tol real 0.01 Tolerance<br><br>Opening file pull1.pdo.gz.<br>-------------------------------------------------------
<br>Program g_wham, VERSION 3.3.1<br>Source code file: gmx_wham.c, line: 90<br><br>Fatal error:<br>This does not appear to be a valid pdo file<br><br><br><br>Can you please let me know how to handle this???<br>Appreciate your help.
<br><br>Thanks,<br>SK<br><br>-------------------------------------------------------<br><br><br><br><br><div><span class="gmail_quote">On 7/3/07, <b class="gmail_sendername">Arneh Babakhani</b> <<a href="mailto:ababakha@mccammon.ucsd.edu">
ababakha@mccammon.ucsd.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">You have to collect all of the pdo files into one directory (and so you'll
<br>have to rename them if they all have identical names). Then zip them<br>using gzip: gzip *.pdo<br><br>Then you can use the g_wham code, something like:<br>g_wham *.gz -bins 1000 -temp 300 -auto<br><br><br><br>>> Hey Mark,
<br>>> Appreciate your immediate response.You can find the input and<br>>> the<br>>> error below:<br>>> g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo<br>>> pull5.pdo
<br>><br>> g_wham -h suggests that -hist won't accept multiple input files. Only a<br>> few GROMACS utilities will do magic concatenation for you. Have a look at<br>> the file format and see what you need to do with a text editor or command
<br>> line tools.<br>><br>>> Opening file pull2.pdo.<br>>><br>>> gunzip: stdin: not in gzip format<br>>> -------------------------------------------------------<br>>> Program g_wham, VERSION
3.3.1<br>>> Source code file: gmx_wham.c, line: 90<br>>><br>>> Fatal error:<br>>> This does not appear to be a valid pdo file<br>>> -------------------------------------------------------<br>
><br>> Does g_wham -o pmf.xvg -hist pull1.pdo work?<br>><br>> Mark<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
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