<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Dear gmx-users,<br ><br >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:<br >-==============================================<br ><SPAN STYLE="font-style: italic;">Option Type Value Description</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">------------------------------------------------------</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-[no]h bool no Print help info and quit</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-nice int 19 Set the nicelevel</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-b time 0 First frame (ps) to read from trajectory</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-e time 0 Last frame (ps) to read from trajectory</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-dt time 0 Only use frame when t MOD dt = first time (ps)</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-tu enum ps Time unit: ps, fs, ns, us, ms or s</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-[no]w bool no View output xvg, xpm, eps and pdb files</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-[no]xvgr bool yes Add specific codes (legends etc.) in the output</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> xvg files for the xmgrace program</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">-sss string HEBT Secondary structures for structure count</SPAN><br style="font-style: italic;" ><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Reading file 1azt_md_grompp.tpr, VERSION 3.3.3 (single precision)</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Reading file 1azt_md_grompp.tpr, VERSION 3.3.3 (single precision)</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Opening library file /usr/local/gromacs/share/gromacs/top/phbres.dat</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 0 ( System) has 12245 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 1 ( Protein) has 217 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 2 ( Protein-H) has 161 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 3 ( C-alpha) has 18 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 4 ( Backbone) has 54 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 5 ( MainChain) has 72 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 6 (MainChain+Cb) has 91 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 7 ( MainChain+H) has 92 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 8 ( SideChain) has 125 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 9 ( SideChain-H) has 88 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 10 ( Prot-Masses) has 217 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 11 ( Non-Protein) has 12028 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 12 ( SOL) has 12027 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 13 ( CL-) has 1 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Group 14 ( Other) has 12028 elements</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Select a group: 5</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Selected 5: 'MainChain'</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">There are 18 residues in your selected group</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Opening library file /usr/local/gromacs/share/gromacs/top/ss.map</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">trn version: GMX_trn_file (single precision)</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Reading frame 0 time 0.000 </SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Back Off! I just backed up ddIuI8uU to ./#ddIuI8uU.1#</SPAN><br style="font-style: italic;" >=================================================<br ><br >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. <br ><br >sharada<br ></BODY></HTML>