<span class="Apple-style-span" style="color: rgb(51, 51, 51); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); "><div><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">Dear Gromacs users,</span></div>
<span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); "><div><span style="color: rgb(51, 51, 51); font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); "><br>
</span></div>First of all, many thanks to Justin for his assistance with my previous question.<div><br></div><div>I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try to preprocess, I get the following output: </div>
<div><br></div><div><div>WARNING 1 [file ffbonded.itp, line 58]:</div><div> Overriding Bond parameters.</div><div><br></div><div> old: 0.1229 476976 0.1229 476976</div><div> new: C O 1 0.13270 179075.2</div>
<div><br></div><div><br></div><div>WARNING 2 [file ffbonded.itp, line 64]:</div><div> Overriding Bond parameters.</div><div><br></div><div> old: 0.1522 265266 0.1522 265266</div><div> new: C CT 1 0.14950 265265.6</div>
<div><br></div><div><br></div><div>WARNING 3 [file ffbonded.itp, line 67]:</div><div> Overriding Bond parameters.</div><div><br></div><div> old: 0.149 334720 0.149 334720</div><div> new: CA C 1 0.14240 392459.2</div>
<div><br></div><div><br></div><div>WARNING 4 [file ffbonded.itp, line 73]:</div><div> Overriding Bond parameters.</div><div><br></div><div> old: 0.1419 374050 0.1419 374050</div><div> new: C CB 1 0.14240 392459.2</div>
<div><br></div><div><br></div><div>-------------------------------------------------------</div><div>Program grompp, VERSION 4.5.4</div><div>Source code file: topdirs.c, line: 76</div><div><br></div><div>Fatal error:</div>
<div>Invalid bond type 0</div><div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank" style="color: rgb(61, 84, 89); ">http://www.gromacs.org/Documentation/Errors</a></div>
</div><div><br></div><div><br></div><div>The error is rather cryptic, and I'm having trouble tracking it down... I even went to the source code (topdirs.c), but I'm still not sure where exactly this "invalid bond type" is being defined. </div>
<div><br></div><div>Thank you so much for your help,</div><div>Olivia</div></span></span><br clear="all"><div><br></div>-- <br><div>Olivia Waring (王维娅)</div>
<div>Princeton University '12</div>
<div>AB Chemistry</div><br>