<DIV> </DIV><DIV> </DIV><SPAN>On 28/02/12, <B class=name>Banafsheh Mehrazma </B><bmehrazma@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CADNrWT4WZi699n3GVuNR1PuSjMTfzKi2oo6oqnfQHyEJkgBWBQ@mail.gmail.com type="cite">
<DIV class="mimepart text html"> 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 style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>SG<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>CYS<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>SG<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>0.2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>CYS2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>CYS2</DIV><DIV>CYS<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>SG<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEM <SPAN style="WHITE-SPACE: pre" class=Apple-tab-span></SPAN>FE<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>0.25<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>CYS2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEME</DIV><DIV>CYS<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>SG<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEM <SPAN style="WHITE-SPACE: pre" class=Apple-tab-span></SPAN>CAB<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>0.18<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>CYS2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEME</DIV><DIV>CYS<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>SG<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEM <SPAN style="WHITE-SPACE: pre" class=Apple-tab-span></SPAN>CAC<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>0.18<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>CYS2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEME</DIV><DIV>HIS<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>NE2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEM <SPAN style="WHITE-SPACE: pre" class=Apple-tab-span></SPAN>FE<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>0.2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HIS1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEME</DIV><DIV>MET<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>SD<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>HEM <SPAN style="WHITE-SPACE: pre" class=Apple-tab-span></SPAN>FE<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>1<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>0.24<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>MET<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </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 style="WHITE-SPACE: pre" class=Apple-tab-span></SPAN>P<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>DT<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>O3'<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>2<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>0.161<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>8OG<SPAN style="WHITE-SPACE: pre" class=Apple-tab-span> </SPAN>DT</DIV></DIV><DIV>...................................................................................................................................</DIV><DIV>or maybe not. Any suggestions will be really appreciated. :)</DIV></DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>We don't have enough information to suggest anything. If the only difference really is the order of non-terminal amino acids, then your symptoms seem impossible. You should look at line 2304 and work backwards.</DIV><DIV> </DIV><DIV>Mark </DIV>