Re: [gmx-users] Gromacs Installation
1. Seems the default fftw configuration is double, when you install the fftw-3.2.2 configure with --enable single. 2. about your question:I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager? 1] You can download in your home directory and install. 2] a better but a bit not so-easy way, is download the source ( http://packages.debian.org/sid/gromacs), built the package and add it into repository. There maybe also some other ways. HTH, lina On Tue, Feb 15, 2011 at 6:23 AM, majid hasan pu_majidha...@yahoo.comwrote: Dear All, I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in my home folder following the instructions on http://www.gromacs.org/Downloads/Installation_Instructions. However, when I do make, I get an error in the end (pasted below). I have also attached the log file of compilation with the email. /usr/bin/ld: /home/majid/user/soft/fftw/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /home/majid/user/soft/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/majid/user/down/gromacs/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/majid/user/down/gromacs/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/majid/user/down/gromacs/src' make: *** [all-recursive] Error 1 Moreover, I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager? Thanks, Majid -- Never miss an email again! Yahoo! Toolbarhttp://us.rd.yahoo.com/evt=49938/*http://tools.search.yahoo.com/toolbar/features/mail/alerts you the instant new Mail arrives.Check it out.http://us.rd.yahoo.com/evt=49937/*http://tools.search.yahoo.com/toolbar/features/mail/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] add force field
I do believe so. ^_^ it works beautifully with the newly-added force field. Thanks, lina On Wed, Feb 9, 2011 at 5:11 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/02/2011 7:47 PM, lina zhao wrote: Hi, it works before I thought it might share some similarity with 4.0.7 which some bash file helps to update the ff information. The mechanism changed in 4.5. Now forcefield.* files do something significant. Look at the contents and see. Mark Thanks, lina On Wed, Feb 9, 2011 at 4:02 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-02-09 08.56, lina zhao wrote: Hi, Anyone has successfully tried to add some new force field in the default force field (in 4.5) so pdb2gmx can show up the (newly-added) force field which will also be recognized by gromacs, Thanks, lina Yes it's easy technically. Just copy e.g. oplsaa.ff to new.ff and edit the files in that directory (not easy). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] add force field
Hi, Anyone has successfully tried to add some new force field in the default force field (in 4.5) so pdb2gmx can show up the (newly-added) force field which will also be recognized by gromacs, Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dssp problem
http://biskit.pasteur.fr/install/applications/dssp wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip unzip dsspcmbi.zip cd dssp ./DsspCompileGCC cd .. sudo mv dssp /usr/local/src/ cd /usr/local/bin sudo ln -s ../src/dssp/dsspcmbi . lina On Sat, Dec 25, 2010 at 8:45 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/12/2010 11:03 PM, mustafa bilsel wrote: Hi Justin, maybe I am making a mistake with installation. What I am doing is this: I am creating a diretory called DSSP, then I write rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/m/DSSP/ on the terminal, and then file transfer starts. Then I write export DSSP=/home/m/DSSP/dssp (pointing the exe file). In above procedures there is NO INSTALLATION. If any installation is required? We don't support DSSP. Please read their instructions and follow them. If you can't follow them, please communicate the problem to them so they can fix it. Another important thing is that I couldn't copy dssp to anywhere with copy dssp /. command, but I can do it cp -r dssp / It means that dssp isnot a file, it seems a folder. And I also see uncompressed zip explanation near the dssp. OK, so if it's a folder, open it and look for the executable to work out its fully-qualified name... I have written axactly what I did so far. No, you've used some frustrating ellipses, instead of copying and pasting from your terminal, thereby leaving us the option of presuming you've done something wrong. Mark Maybe it will help you to understand the mistake. Thank you for your kind interests best wishes Mustafa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
