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