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! >>Please don't post (un)subscribe requests to the list. Use the >>www interface or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >_______________________________________________ >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! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to [EMAIL PROTECTED] >Can't post? Read http://www.gromacs.org/mailing_lists/users.php _________________________________________________________________ 与联机的朋友进行交流,请使用 Live Messenger; http://get.live.com/messenger/overview _______________________________________________ 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php