Hi..<br> I listed all the zipped files separately as you said.<br><br> g_wham -bins 1000 pull1.pdo.gz pull2.pdo.gz pull3.pdo.gz pull4.pdo.gz pull5.pdo.gz -temp 298 -o pmf.xvg<br><br>I still have the same problem.<br> :-) G R O M A C S (-:
<br><br> GRoups of Organic Molecules in ACtion for Science<br><br> :-) VERSION 3.3.1 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2006, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org
</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2
<br> of the License, or (at your option) any later version.<br><br> :-) g_wham (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------
<br> -o pmf.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>That is the error which I get....
<br>Thank You for your input..<br>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.<br>Thanks,<br>SK
<br><br><br><div><span class="gmail_quote">On 7/3/07, <b class="gmail_sendername">Lu Lanyuan</b> <<a href="mailto:lulanyuan@msn.com">lulanyuan@msn.com</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;">
I just zipped alll the *.pdo files seperately and listed them all when<br>using g_wham. It's like g_wham <options> pull1.pdo.gz pull2.pdo.gz ... In<br>the old gromacs versions like 3.1.4, the g_wham was broken and I was using
<br>a version modifined by David Bostick. You can search the mailing list for<br>that information. I'm not sure whether the old problem of g_wham was fixed<br>in 3.3.1.<br>Lanyuan Lu<br><br><br>>From: "Sudha Mani Karra" <
<a href="mailto:karra.md@gmail.com">karra.md@gmail.com</a>><br>>Reply-To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>To: "Discussion list for GROMACS users" <
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>Subject: Re: [gmx-users] g_wham and PMF problem<br>>Date: Tue, 3 Jul 2007 10:08:33 -0500<br>><br>>Hi Mark,<br>> when I give only one file in the input for g_wham,
<br>><br>>g_wham -o pmf.xvg -hist pull1.pdo ,<br>><br>>It asks me to give a series of inputs.The error which I get is<br>> :-) g_wham (-:<br>><br>>Option Filename Type Description<br>
>------------------------------------------------------------<br>> -o pmf.xvg Output xvgr/xmgr file<br>>-hist pull1.pdo.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<br>>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 100 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>>-------------------------------------------------------<br>>Program g_wham, VERSION 3.3.1<br>>Source code file: gmx_wham.c, line: 314
<br>><br>>Fatal error:<br>>You need to specify a series of pdo files as input<br>>---------------------------------------------------<br>><br>>Appreciate your help.Thanks,<br>>SK<br>><br>><br>>
<br>><br>><br>><br>><br>>On 7/3/07, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:<br>>><br>>> > Hey Mark,<br>>> > Appreciate your immediate
response.You can find the<br>>>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.
<br>>>Only a<br>>>few GROMACS utilities will do magic concatenation for you. Have a<br>>>look at<br>>>the file format and see what you need to do with a text editor or<br>>>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</a><br>>><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>>Please search the archive at <a href="http://www.gromacs.org/search">
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