dear Mark; <div>I forgot to mention that the O3' in the next residue (a native thymine) that is bonded to P in modified base, is changed to atom type OH instead of being OS.</div><div>However in the dna.rtp file, for [ DT ] O3' is OS, not OH.</div>
<div>and the line 2304 is the angle P OH C3', which we don't have in the ffbonded.itp. But we have P OS C3'.</div><div>I have no idea why the gromacs is reading the O3', OH instead of OS!</div><div><br></div>
<div>Thank you</div><div>Banafsheh</div><div><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 12:46 PM, Banafsheh Mehrazma <span dir="ltr"><<a href="mailto:bmehrazma@gmail.com">bmehrazma@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> 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-wrap"> </span>SG<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>CYS<span style="white-space:pre-wrap"> </span>SG<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>0.2<span style="white-space:pre-wrap"> </span>CYS2<span style="white-space:pre-wrap"> </span>CYS2</div>
<div>CYS<span style="white-space:pre-wrap"> </span>SG<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>HEM <span style="white-space:pre-wrap"> </span>FE<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>0.25<span style="white-space:pre-wrap"> </span>CYS2<span style="white-space:pre-wrap"> </span>HEME</div>
<div>CYS<span style="white-space:pre-wrap"> </span>SG<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>HEM <span style="white-space:pre-wrap"> </span>CAB<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>0.18<span style="white-space:pre-wrap"> </span>CYS2<span style="white-space:pre-wrap"> </span>HEME</div>
<div>CYS<span style="white-space:pre-wrap"> </span>SG<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>HEM <span style="white-space:pre-wrap"> </span>CAC<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>0.18<span style="white-space:pre-wrap"> </span>CYS2<span style="white-space:pre-wrap"> </span>HEME</div>
<div>HIS<span style="white-space:pre-wrap"> </span>NE2<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>HEM <span style="white-space:pre-wrap"> </span>FE<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>0.2<span style="white-space:pre-wrap"> </span>HIS1<span style="white-space:pre-wrap"> </span>HEME</div>
<div>MET<span style="white-space:pre-wrap"> </span>SD<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>HEM <span style="white-space:pre-wrap"> </span>FE<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>0.24<span style="white-space:pre-wrap"> </span>MET<span style="white-space:pre-wrap"> </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-wrap"> </span>P<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>DT<span style="white-space:pre-wrap"> </span>O3'<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>0.161<span style="white-space:pre-wrap"> </span>8OG<span style="white-space:pre-wrap"> </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>
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