Re: [gmx-users] DSSP installation on Ubuntu 12.10

2013-10-11 Thread Justin Lemkul
On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd

Re: [gmx-users] DSSP installation on Ubuntu 12.10

2013-10-11 Thread Mass
Hi Justin, Sorry for the mistake, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error,  Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line:

Re: [gmx-users] DSSP installation on Ubuntu 12.10

2013-10-11 Thread Justin Lemkul
On 10/11/13 8:12 AM, Mass wrote: Hi Justin, Sorry for the mistake, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file:

Re: [gmx-users] DSSP installation on Ubuntu 12.10

2013-10-11 Thread Mass
Dear Gromacs user, Can anyone tell me how  to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? Thanks On Saturday, October 12, 2013 1:12 AM, Mass

Re: [gmx-users] DSSP installation on Ubuntu 12.10

2013-10-11 Thread Justin Lemkul
On 10/11/13 8:57 AM, Mass wrote: Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? It depends on your shell. In

Re: [gmx-users] DSSP installation on Ubuntu 12.10

2013-10-11 Thread Mark Abraham
Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue. Google knows a lot more about it than anybody here ;-) Mark On Fri, Oct 11, 2013 at 2:57 PM, Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source

Re: [gmx-users] DSSP installation on Ubuntu 12.10

2013-10-10 Thread Mark Abraham
Hi, Since the release of 4.5.5, DSSP totally changed its command-line interface. So old GROMACS code cannot work with new DSSP. You need to get the old version of DSSP to use with old GROMACS, or new GROMACS code to work with either DSSP. Mark On Thu, Oct 10, 2013 at 1:37 PM, Mass

Re: [gmx-users] DSSP installation on Ubuntu 12.10

2013-10-10 Thread Mass
Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON