<div>Dear Justin, </div>
<div>Regarding our previous discussion under "CNT" topic, you want to know exactly what I did to define C-C interaction. I have summarized it below. </div>
<div> </div>
<div>1. I copied oplsaa.ff folder in my working directory</div>
<div>2. I added following lines to atomname2type.n2t</div>
<div><font color="#000000"><font color="#330033"><span style="COLOR: rgb(255,102,102)">C opls_995 0 12.011 2 C 0.142 C 0.142</span><br style="COLOR: rgb(255,102,102)"><span style="COLOR: rgb(255,102,102)">C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142</span><br style="COLOR: rgb(255,102,102)">
<span style="COLOR: rgb(255,102,102)">C opls_997 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142</span><br style="COLOR: rgb(255,102,102)"><span style="COLOR: rgb(255,102,102)">C opls_998 0 12.011 5 C 0.142 C 0.142 C 0.142 C 0.142 C 0.142</span></font><br>
</font></div>
<div><font color="#000000">3. I added those to atomtypes.atp</font></div>
<div> opls_995 12.01100 ; <br> opls_996 12.01100 ; </div>
<div> opls_997 12.01100 ; <br> opls_998 12.01100 ; </div>
<div> </div>
<div>4. I added those to ffbonded.itp</div>
<div>[ bondtypes ]<br> C C 1 0.14210 478900<br> [ angletypes ]<br> C C C 1 120.000 562.2<br> [ dihedraltypes ]<br></div>
<div>5. I constructed .top file for CNT with the following, then I converted it into .itp by vi editor</div>
<div><span style="COLOR: rgb(255,102,102)">g_x2top -f cnt.gro -o cnt.top -nopairs -nexcl 5</span><br></div>
<div>6. By pdb2gmx, I obtained .top for peptide then I converted it into .itp <br>7. I combined CNT and peptide's pdbs in pymol and saved.</div>
<div>8. I wrote a .top file given below,</div>
<div>;<br>; File 'topol.top' was generated<br>; By user: onbekend (0)<br>; On host: onbekend<br>; At date: Mon Jan 10 02:51:19 2011<br>;<br>; This is a standalone topology file<br>;<br>; It was generated using program:<br>
; pdb2gmx - VERSION 4.5.3<br>;<br>; Command line was:<br>; pdb2gmx -ignh -f vpgvg10.pdb <br>;<br>; Force field was read from the standard Gromacs share directory.<br>;</div>
<div>; Include forcefield parameters<br>#include "forcefield.itp"</div>
<div><br>; Include topology for CNT<br>#include "cnt.itp"</div>
<div>; Include topology for UW1<br>#include "uw1.itp"</div>
<div>; Include water topology<br>#include "spc.itp"</div>
<div>[ system ]<br>; Name<br>Protein and CNT in water</div>
<div>[ molecules ]<br>; Compound #mols<br>Protein 1<br>CNT 1<br>SOL 4019 </div>
<div>9. When I make grompp for minimization it givea me the following error</div>
<div>WARNING 1 [file ffbonded.itp, line 2703]:<br> Overriding Bond parameters.</div>
<div> old: 0.151 292880 0.151 292880 <br> new: C C 1 0.14210 478900</div>
<div><br>ERROR 1 [file ffbonded.itp, line 2707]:<br> Not enough parameters</div>
<div>Generated 334153 of the 334153 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 334153 of the 334153 1-4 parameter combinations</div>
<div>-------------------------------------------------------<br>Program grompp, VERSION 4.5.3<br>Source code file: toppush.c, line: 1166</div>
<div>Fatal error:<br>Atomtype opls_996 not found<br></div>
<div> </div>
<div>That is all what I exactly did. Is anything wrong or missing?</div>
<div> </div>
<div>best wishes</div>
<div>trevor</div>
<div> </div>
<div><br> </div>