Hi,<br><br>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:<br>
<br>processing topology...<br>Generated 716 of the 2628 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 1<br>Generated 1046 of the 2628 1-4 parameter combinations<br>WARNING 1 [file "insu_pwi.top", line 607]:<br>
No default G96Bond types, using zeroes<br>WARNING 2 [file "insu_pwi.top", line 745]:<br> No default G96Bond types, using zeroes<br>WARNING 3 [file "insu_pwi.top", line 2008]:<br> No default G96Angle types, using zeroes<br>
WARNING 4 [file "insu_pwi.top", line 2209]:<br> No default G96Angle types, using zeroes<br>WARNING 5 [file "insu_pwi.top", line 2345]:<br> No default G96Angle types, using zeroes<br>WARNING 6 [file "insu_pwi.top", line 2512]:<br>
No default G96Angle types, using zeroes<br>WARNING 7 [file "insu_pwi.top", line 2748]:<br> No default Proper Dih. types, using zeroes<br>WARNING 8 [file "insu_pwi.top", line 2820]:<br> No default Proper Dih. types, using zeroes<br>
WARNING 9 [file "insu_pwi.top", line 2863]:<br> No default Proper Dih. types, using zeroes<br>WARNING 10 [file "insu_pwi.top", line 2919]:<br> No default Proper Dih. types, using zeroes<br>Cleaning up temporary file gromppID2O6e<br>
-------------------------------------------------------<br>Program grompp, VERSION 3.3.1<br>Source code file: fatal.c, line: 416<br><br>Fatal error:<br>Too many warnings, /usr/local2/gromacs/bin/grompp terminated<br>-------------------------------------------------------<br>
<br>"Encountered Subspace Anomaly" (Star Trek)<br><br>MD_insu.tpr was not created. Check for errors. Exiting ... <br><br>Is there a way to fix it ? Also what are those b_, ga_. gd_ corresponds to ??<br><br>Ram.<br>
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