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<div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><br><div> Dear Justin and All</div><div><br></div><div><br> Right now, I am trying to add new residue in OPLS-aa ff<br><br> when I make the following grompp -f file.mdp -c file.gro -p file.top -o file<br><br> I have the following error<br>> --------------------<br>> Program grompp, VERSION 4.5.2<br>> Source code file: toppush.c, line: 1071<br>> <br>> Fatal error:<br>> Atoms in the .top are not numbered consecutively from 1 (rather,<br>> atomnr = -89390831, while at->nr = 0)<br>> For more information and tips for troubleshooting, please check the GROMACS<br>> website at http://www.gromacs.org/Documentation/Errors-<br>> ----------------</div><div><br> These are my files<br><br><br> <font color="#ff0000"><b>0- file forcefiel.itp</b></font></div><div><font color="#ff0000"><b><br></b></font> [ defaults ]<br> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br> 1 3 yes 0.5 0.5<br> </div><div><br></div><div> <font color="#ff0000"><b>1- file.rtp</b></font><br><br> ; Ion thiocyanate adiciionado<br> [ SCN ]<br> [ atoms ]<br> SQ opls_966 -0.750 1<br> CQ opls_967 0.490 1<br> NQ opls_968 -0.740 1<br> [ bonds ]<br><br> CQ SQ<br> CQ NQ<br><br><br></div><div> <font color="#ff0000"><b>2- file.atp</b></font><br><br> opls_966 32.06000 ; SQ (SCN-)<br> opls_967 12.01100 ; CQ (SCN-)<br> opls_968 14.00670 ; NQ (SCN-)<br><br><br><font color="#ff0000"><b> 3- file ffbonded.itp</b></font><br><br> [ bondtypes ]<br> ; i j func b0 kb<br> CQ SQ 1 0.16700 284082.0 ; JChemPhys_2008_118_154504<br> CQ NQ 1 0.11900 <b>122389e1</b> ; JChemPhys_2008_118_154504<br><br> [ angletypes ]<br> ; i j k func th0 cth<br><br> SQ CQ NQ 1 180.000 652.802 ;JChemPhys_2008_118_154504<br><br><b> <font color="#ff0000">4- file ffnonbonded.itp</font></b><br> [ atomtypes ]<br> ; full atom descriptions are available in ffoplsaa.atp<br> ; name bond_type mass charge ptype sigma epsilon<br> opls_966 SQ 16 32.06000 -0.750 A 3.55000e-01 1.04600e+00<br> opls_967 CQ 6 12.01100 0.490 A 3.75000e-01 4.39320e-01<br> opls_968 NQ 7 14.00670 -0.740 A 3.25000e-01 7.11280e-01<br><br><br><font color="#ff0000"><b>5. file minimization.mdp</b></font><br><br> ; Minimization<br> integrator = steep<br> emtol = 1000.0<br> emstep = 0.01<br> nsteps = 50000<br> dt = 0.01<br> ns_type = grid<br> pbc = xyz<br> ;Electrostatic<br> coulombtype = PME</div><div> pme_order = 4<br> fourierspacing = 0.12<br> rcoulomb = 0.9<br> rvdw = 0.9<br> </div><div><br></div><div> <font color="#ff0000"><b>6. file .gro</b></font><br> SCN THIOCYANATE ION<br> 3<br> 1SCN SQ 1 1.720 1.647 1.785<br> 1SCN CQ 2 1.640 1.651 1.631<br> 1SCN NQ 3 1.590 1.653 1.534<br> 3.30000 3.30000 3.30000</div><div><font color="#ff0000"><b><br></b></font></div><div><font color="#ff0000"><b><br></b></font></div><div><font color="#ff0000"><b> 7 file.top</b></font><br><br><span style="font-size:10pt"> [ moleculetype ]</span></div><div> ; Name nrexcl<br> Ion 3<br><br> [ atoms ]<br> ; nr type resnr residue atom cgnr charge mass typeB ch<br> argeB massB<br> ; residue 1 SCN rtp SCN q -1.0<br> 1 opls_966 1 SCN SQ 1 -0.75 32.06 ; qtot -0.<br> 75<br> 2 opls_967 1 SCN CQ 1 0.49 12.011 ; qtot -0.<br> 26<br> 3 opls_968 1 SCN NQ 1 -0.74 14.0067 ; qtot -1<br><br> [ bonds ]<br> ; ai aj funct c0 c1 c2 c3<br> 1 2 1<br> 2 3 1<br><br> [ angles ]<br> ; ai aj ak funct c0 c1 c2 c3<br> 1 2 3 1<br> ; Include topology for ions<br> #include "./modif.ff/ions.itp"<br><br> [ system ]<br> ; Name<br> SCN THIOCYANATE ION<br><br> [ molecules ]<br> ; Compound #mols<br> Ion 1<br><br><br> Thanks,<br></div><div><br></div><div>Ana Gomez</div><div>Student</div>                                            </div></div>                                            </div></div>                                            </div>
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