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 > > _______________________________________________ > 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
_______________________________________________ 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