<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Why don't you simply define a extra bond between your two CYS side chains beads? <div><br><div><div>On May 13, 2010, at 3:31 PM, Anna Duncan wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div>I'm trying to energy minimise a protein structure. In one area of the structure there are some salt bridges and when I do an energy minimisation without any restraints these are disrupted, which is something I want to avoid. To that end, I've tried restraining the residues that are involved, first with position restraints and then with distance restraints, but in both cases I get a segmentation fault in the same place.</div><div>The command I issue looks like:</div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">grompp -f em.mdp -c 1okc_ex.cg.gro -p 1okc_ex.top -o 1okc_min_sbRes -v -n salt_bridges.ndx</span></font></font></div><div><br></div><div>and the output:</div><div><div>I<font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px; ">gnoring obsolete mdp entry 'title'</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Ignoring obsolete mdp entry 'cpp'</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Replacing old mdp entry 'unconstrained_start' by 'continuation'</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">checking input for internal consistency...</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">NOTE 1 [file em.mdp, line unknown]:</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> For energy conservation with switch/shift potentials, rlist should be 0.1</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> to 0.3 nm larger than rcoulomb.</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">NOTE 2 [file em.mdp, line unknown]:</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> For energy conservation with switch/shift potentials, rlist should be 0.1</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> to 0.3 nm larger than rvdw.</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">processing topology...</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Generated 0 of the 465 non-bonded parameter combinations</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Segmentation fault</span></font></font></div><div><br></div><div>--------------------------------------------------------------------------------------</div><div><br></div></div><div>Like I say, when I do this without the restraints, grompp and mdrun run fine. The only differences, then, between the input is the line in em.mdp:</div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;">define = -DDISTRESB</span></font></div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">The topoolgy file, 1okc_ex.top looks like:</span></font></div><div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">#include "martini_v2.1.itp"</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">#include "1okc_ex.itp"</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">#ifdef POSRESB</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">#include posre_saltbridges.itp</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">#endif</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">#ifdef DISTRESB</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">#include distre_sb.itp</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">#endif</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">[ system ]</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">1OKC_EX SIMULATION</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">[ molecules ]</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Protein 1</span></font></font></div><div><br></div><div>--------------------------------------------------------------------------------------</div><div><br></div><div>The position restraints file looks like: </div><div><div>;<font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> position restraints for r_28_r_31_r_133_r_136_r_230_r_233 of God Rules Over Mankind, Animals, Cosmos and Such</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">[ position_restraints ]</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">; i funct fcx fcy fcz</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 52 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 53 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 59 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 60 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 61 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 296 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 297 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 303 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 304 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 305 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 505 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 506 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 511 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 512 1 1000 1000 1000</span></font></font></div><div><font class="Apple-style-span" face="Monaco"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 513 1 1000 1000 1000</span></font></font></div><div><br></div><div>--------------------------------------------------------------------------------------</div><div><br></div><div>and the distance restraints file looks like:</div><div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;">; distance restraints for h1-h3_sb of God Rules Over Mankind, Animals, Cosmos and Such</span></font></div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;">[ distance_restraints ]</span></font></div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;">; i j ? label funct lo up1 up2 weight</span></font></div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 53 395 1 0 1 2.00181 2.20181 3.20181 1</span></font></div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 297 513 1 0 1 0.462702 0.662702 1.6627 1</span></font></div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;"> 61 506 1 0 1 0.3818 0.5818 1.5818 1</span></font></div><div><br></div></div><div><div>--------------------------------------------------------------------------------------</div><div><br></div><div><br></div><div>I can't work out what is giving the segmentation fault because I think the restraint files are in the right format and I can't think of what else would go wrong at this stage for a segmentation fault to occur.</div><div><br></div><div>In the grompp run that works (without any restraints) the line after where the segmentation error occurs in the other cases looks like:</div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;">Excluding 1 bonded neighbours molecule type 'Protein'</span></font></div><div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div>Many thanks,</div><div>Anna</div></div></div><div><br></div></div></div>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></body></html>