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
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