Dear all;<div>I have used a modified guanine in my simulation before, with new parameters added in amber99 force field and there was no error through the whole simulation. now I'm trying to do a simulation with modified Guanine on a different sequence of the DNA with the same commands;</div>
<div><div> pdb2gmx -f modified.pdb -o DNA.gro</div><div> editconf -f DNA.gro -o DNA_newbox.gro -c -d 1.0 -bt cubic</div><div> genbox -cp DNA_newbox.gro -cs spc216.gro -o DNA_solv.gro -p topol.top</div>
<div>but when I run this one;</div><div> grompp -f ions.mdp -c DNA_solv.gro -p topol.top -o ions.tpr</div><div> there is this error</div></div><div><div> ERROR [file topol_DNA_chain_A.itp, line 2304]:</div>
<div> No default Angle types</div></div><div>so when I checked the topology files, I saw that for the next residue after the modified guanine, the O3' has a H3T (bonded to H terminal, which I don't know where this did came from) and another bond to P of modified guanine (which should have). I guess, gromacs recognized it as a terminal base, however it has the linkage to the next base, as well.</div>
<div><br></div><div>The only difference between my last dna and this one, is that in the last one the modification was in the 2nd position but this one is in the fourth. </div><div><br></div><div>I think there may be a problem with my specbond.dat :</div>
<div>................................................................................................................................. </div><div><div>9</div><div>CYS<span class="Apple-tab-span" style="white-space:pre"> </span>SG<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>CYS<span class="Apple-tab-span" style="white-space:pre"> </span>SG<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>0.2<span class="Apple-tab-span" style="white-space:pre"> </span>CYS2<span class="Apple-tab-span" style="white-space:pre"> </span>CYS2</div>
<div>CYS<span class="Apple-tab-span" style="white-space:pre"> </span>SG<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>HEM <span class="Apple-tab-span" style="white-space:pre"> </span>FE<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span>0.25<span class="Apple-tab-span" style="white-space:pre"> </span>CYS2<span class="Apple-tab-span" style="white-space:pre"> </span>HEME</div>
<div>CYS<span class="Apple-tab-span" style="white-space:pre"> </span>SG<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>HEM <span class="Apple-tab-span" style="white-space:pre"> </span>CAB<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>0.18<span class="Apple-tab-span" style="white-space:pre"> </span>CYS2<span class="Apple-tab-span" style="white-space:pre"> </span>HEME</div>
<div>CYS<span class="Apple-tab-span" style="white-space:pre"> </span>SG<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>HEM <span class="Apple-tab-span" style="white-space:pre"> </span>CAC<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>0.18<span class="Apple-tab-span" style="white-space:pre"> </span>CYS2<span class="Apple-tab-span" style="white-space:pre"> </span>HEME</div>
<div>HIS<span class="Apple-tab-span" style="white-space:pre"> </span>NE2<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>HEM <span class="Apple-tab-span" style="white-space:pre"> </span>FE<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>0.2<span class="Apple-tab-span" style="white-space:pre"> </span>HIS1<span class="Apple-tab-span" style="white-space:pre"> </span>HEME</div>
<div>MET<span class="Apple-tab-span" style="white-space:pre"> </span>SD<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>HEM <span class="Apple-tab-span" style="white-space:pre"> </span>FE<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>0.24<span class="Apple-tab-span" style="white-space:pre"> </span>MET<span class="Apple-tab-span" style="white-space:pre"> </span>HEME</div>
<div>CO C 1 HEME FE 1 0.19 CO HEME</div><div>CYM SG 1 CYM SG 1 0.2 CYS2 CYS2</div><div>8OG <span class="Apple-tab-span" style="white-space:pre"> </span>P<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span>DT<span class="Apple-tab-span" style="white-space:pre"> </span>O3'<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span>0.161<span class="Apple-tab-span" style="white-space:pre"> </span>8OG<span class="Apple-tab-span" style="white-space:pre"> </span>DT</div>
</div><div>...................................................................................................................................</div><div>or maybe not. Any suggestions will be really appreciated. :)</div><div>
<br></div><div>Best regards;</div><div>Banafsheh</div><div><br></div><div><br></div><div> </div><div><br></div>