Hi Justin, Thanks for your response. I've attempted to run gmx wham using GROMACS 5.1.4 and I seem to get the same problem, even if I attempt to use dos2unix before I issue a command i.e. ------------------------------------------------------- Program gmx wham, VERSION 5.1.4 Source code file: /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, line: 1800
Fatal error: Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I've taken a look at older posts relating to this problem, and I saw that a similar complaint was resolved after the poster used dos2unix (following your recommendation). But that hasn't seemed to work for me. Regards, ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Tuesday, November 14, 2017 2:35 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem using gmx wham At least upgrade to the latest release in the series (5.1.4) or better yet, the actual latest version (2016.4) to see if this is a bug that's been fixed. I seem to recall this same behavior reported before and subsequently solved, but haven't dug it up. -Justin On 11/13/17 7:11 AM, Jefferies D.F. wrote: > Hey guys, > > Sorry if it seems that I'm bumping this thread, but I was wondering if anyone > had any other suggestions before I let this thread die. > > Thanks. > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies > D.F. [dfj1...@soton.ac.uk] > Sent: Thursday, November 02, 2017 1:29 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problem using gmx wham > > Hi Justin, > > Thanks for the response. The .dat files were created with the vi text editor, > they contain lists of the .tpr and .xvg to be read, e.g. > > umbrella0.tpr > umbrella1.tpr > umbrella2.tpr > .. > umbrella52.tpr > > I've tried to use dos2unix, i.e. > ~> dos2unix tpr-files.dat > and > ~> dos2unix pullf-files.dat > > but I still get the same error message i.e. > > ------------------------------------------------------- > Program gmx wham, VERSION 5.1.2 > Source code file: > /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: > 1800 > > Fatal error: > Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > That being said, it seems you're correct in thinking something's weird with > the input files. After I created new .dat files, I got this message: > > ------------------------------------------------------- > Program gmx wham, VERSION 5.1.2 > Source code file: > /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: > 3610 > > Fatal error: > Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > gmx wham is registering 54 files, when only 53 were written. > > > > > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin > Lemkul [jalem...@vt.edu] > Sent: Thursday, November 02, 2017 11:10 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problem using gmx wham > > On 11/1/17 4:26 PM, Jefferies D.F. wrote: >> Hi, >> >> I am attempting to use gmx wham to compute a potential of mean force. I have >> used the command line: >> >> gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ >> >> where tpr-files.dat and pullf-files.dat contain a list of the .tpr and >> pullf.xvg files from each umbrella sampling window, respectively. >> >> It seems that gmx wham is having trouble reading the .tpr and .xvg files, as >> I get this error message: >> >> ------------------------------------------------------- >> >> Program gmx wham, VERSION 5.1.4 >> >> Source code file: >> /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, >> line: 1800 >> >> >> Fatal error: >> >> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo. >> > The extra space after "tpr" in the printed error suggests something is > weird with the input .dat file. Did you create it with a proper plain > text editor? What about running dos2unix on it to make sure you've got > the right kind of line endings? > > -Justin > >> For more information and tips for troubleshooting, please check the GROMACS >> >> website at http://www.gromacs.org/Documentation/Errors >> >> ------------------------------------------------------- >> >> >> I have computed potential of mean force profiles before (using this Mac), >> but I haven't encountered this problem. Could someone help me with this >> problem? >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.