[gmx-users] ngmx,dssp not working

sharada sharada at ccmb.res.in
Thu Jun 12 07:58:49 CEST 2008

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. 
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