[gmx-users] Question about installing DSSP on Ubuntu 12.10

I am trying to install DSSP in Ubuntu 12.10, I just download it from Ubuntu software centre but when I run it I am getting the following error, any solution? I have checked all the mail list archive and could not solve my problem Fatal error: Failed to execute command: /usr/local/bin/dssp -na

[gmx-users] DSSP installation on Ubuntu 12.10

Dear Gromacs users, I have asked this questions before and Justin gave some answers which I could solve my problem based on his answer. I am using Ubuntu 12.10 and installed gromacs 4.5.5-2.  this is what I have done 2- I moved this file to usr/local/bin 1- first I downloaded the dssp  wget

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

on this? how can I call gromacs without sourcing every time  secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error  Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src

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

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

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 masstransfer_2

[gmx-users] DSSP problem

Dear users; I am trying to run DSSP and have problem, 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

Re: [gmx-users] DSSP problem

Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l total 92332632 -rw-rw-r-- 1 Mass Mass 0 Sep 8 19:46 310Helix.dat -rw--- 1 Mass Mass 371878 Aug 21 07:39 3BLG_115XrayWater.top -rw-rw-r-- 1 Mass

[gmx-users] Lysozyme in Water at different pH and Ionic strength

Dear Gromacs users, Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please