Hi, I have three di sulphide bonds in my crystal structure. In the topology file it left blanks at the corresponding sulphur connectivities (i.e., values corresponding to gb_, ga_. gd_ ). When I try to create the .tpr file it complains the following:
processing topology... Generated 716 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1046 of the 2628 1-4 parameter combinations WARNING 1 [file "insu_pwi.top", line 607]: No default G96Bond types, using zeroes WARNING 2 [file "insu_pwi.top", line 745]: No default G96Bond types, using zeroes WARNING 3 [file "insu_pwi.top", line 2008]: No default G96Angle types, using zeroes WARNING 4 [file "insu_pwi.top", line 2209]: No default G96Angle types, using zeroes WARNING 5 [file "insu_pwi.top", line 2345]: No default G96Angle types, using zeroes WARNING 6 [file "insu_pwi.top", line 2512]: No default G96Angle types, using zeroes WARNING 7 [file "insu_pwi.top", line 2748]: No default Proper Dih. types, using zeroes WARNING 8 [file "insu_pwi.top", line 2820]: No default Proper Dih. types, using zeroes WARNING 9 [file "insu_pwi.top", line 2863]: No default Proper Dih. types, using zeroes WARNING 10 [file "insu_pwi.top", line 2919]: No default Proper Dih. types, using zeroes Cleaning up temporary file gromppID2O6e ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, /usr/local2/gromacs/bin/grompp terminated ------------------------------------------------------- "Encountered Subspace Anomaly" (Star Trek) MD_insu.tpr was not created. Check for errors. Exiting ... Is there a way to fix it ? Also what are those b_, ga_. gd_ corresponds to ?? Ram.
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