<P>Dear GMX users,<BR><BR>After 1ns MD for my system (protein+drug(RPR)+ Ca2+ +<BR>Cl-), g_hbond -f file.xtc -s file.tpr -num hydrogen.xvg <BR>gave a Segmentation faut (see attached file below) and<BR>then stopped. How to fix the problem?( I use gmx3.2.1,<BR>Linux Red Hat8.0) <BR><BR>Thank you very much for your reply.<BR><BR>Xiaobing<BR><BR>attached file:<BR>No option -da<BR>Reading file ezq_md.tpr, VERSION 3.2.1 (single<BR>precision)<BR>Specify 2 groups to analyze:<BR>Opening library file<BR>/usr/local/share/gromacs/top/aminoacids.dat<BR>Group 0 ( System) has 47436 elements<BR>Group 1 ( Protein) has 2869 elements<BR>Group 2 ( Protein-H) has 2229 elements<BR>Group 3 ( C-alpha) has 285 elements<BR>Group 4 ( Backbone)
has 855 elements<BR>Group 5 ( MainChain) has 1142 elements<BR>Group 6 (MainChain+Cb) has 1400 elements<BR>Group 7 ( MainChain+H) has 1422 elements<BR>Group 8 ( SideChain) has 1447 elements<BR>Group 9 ( SideChain-H) has 1087 elements<BR>Group 10 ( Prot-Masses) has 2869 elements<BR>Group 11 ( Non-Protein) has 44567 elements<BR>Group 12 ( CA) has 1 elements<BR>Group 13 ( RPR) has 42 elements<BR>Group 14 ( SOL) has 44523 elements<BR>Group 15 ( Cl)
has 1 elements<BR>Group 16 ( Other) has 44567 elements<BR>Select a group: 13<BR>Selected 13: 'RPR'<BR>Select a group: 1<BR>Selected 1: 'Protein'<BR>Checking for overlap...<BR>Calculating hydrogen bonds between two groups of 42<BR>and 2869 atoms<BR>Found 4 donors and 7 acceptors in group 'RPR'<BR>Found 419 donors and 817 acceptors in group 'Protein'<BR>Going to allocate 8169 kb of memory, and that's only<BR>the beginning<BR>trn version: GMX_trn_file (single precision)<BR>Reading frame 0 time 0.000<BR>Will do grid-seach on 18x18x18 grid, rcut=0.35<BR>Last frame 250 time 1000.000<BR>Found 13 different hydrogen bonds in trajectory<BR>Merging hbonds with Acceptor and Donor swapped<BR>Segmentation fault (core dumped)<BR>[root@tesla ezq]#<BR></P><BR><BR>Xiaobing Tian Ph.D.<br>Department of Microbiology and
Immunology<br>Thomas Jefferson University<br>1025 Walnut St., Suite 420<br>Philadelphia, PA19107<br>Phone: 215-955-1364 (Lab)<p><hr size=1><font face=arial size=-1>Do you Yahoo!?<br>
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