[gmx-users] ngmx,dssp not working

[Nizamov Shawkat]

>
> Dear gmx-users,
>
> I have installed the gromacs 3.3.3 on a dual core HP workstation with 
> Ubuntu platform. All the programs are properly installed and working 
> except ngmx and dssp. However there is a difference, ngmx is not 
> installed as I donot see the link in /usr/local/bin along with the 
> other programs. where as dssp when executed outputs one pdb file and 
> just hangs for a long time (days) without giving any other output. 
> This is how the output looks:
> -==============================================
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 19 Set the nicelevel
> -b time 0 First frame (ps) to read from trajectory
> -e time 0 Last frame (ps) to read from trajectory
> -dt time 0 Only use frame when t MOD dt = first time (ps)
> -tu enum ps Time unit: ps, fs, ns, us, ms or s
> -[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
> -sss string HEBT Secondary structures for structure count
>
> Reading file 1azt_md_grompp.tpr, VERSION 3.3.3 (single precision)
> Reading file 1azt_md_grompp.tpr, VERSION 3.3.3 (single precision)
> Opening library file /usr/local/gromacs/share/gromacs/top/phbres.dat
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Group 0 ( System) has 12245 elements
> Group 1 ( Protein) has 217 elements
> Group 2 ( Protein-H) has 161 elements
> Group 3 ( C-alpha) has 18 elements
> Group 4 ( Backbone) has 54 elements
> Group 5 ( MainChain) has 72 elements
> Group 6 (MainChain+Cb) has 91 elements
> Group 7 ( MainChain+H) has 92 elements
> Group 8 ( SideChain) has 125 elements
> Group 9 ( SideChain-H) has 88 elements
> Group 10 ( Prot-Masses) has 217 elements
> Group 11 ( Non-Protein) has 12028 elements
> Group 12 ( SOL) has 12027 elements
> Group 13 ( CL-) has 1 elements
> Group 14 ( Other) has 12028 elements
> Select a group: 5
> Selected 5: 'MainChain'
> There are 18 residues in your selected group
> Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
> trn version: GMX_trn_file (single precision)
> Reading frame 0 time 0.000
> Back Off! I just backed up ddIuI8uU to ./#ddIuI8uU.1#
> =================================================
>
> I am unable to figure out the problem. Any suggestions are welcome. 
> About ngmx I tried to install it seperately using make and make 
> install but it does not compile/install. How should I install it ? 
> Thankyou for the time.
>
> sharada
>
How did you installed gromacs on ubuntu ? Looks like it was done manually.
Don't bother with compilation, there is  already a package  for ubuntu 
in its universe repository,
just activate "universe" section and use "sudo apt-get install gromacs".
Current version is gromacs-3.3.3, package contains ngmx and installs all 
binaries to /usr/bin.


Hope, it will help

PS ubuntu 8.04