<br /><br /><span>On 14/03/11, <b class="name">Yulian Gavrilov </b> <zzeppelin87@gmail.com> wrote:</span><blockquote cite="mid:AANLkTinGjZ4-Su-TvmUsBOt1jRc2gFzZdKKC37Eu6gAy@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div dir="ltr">Dear, Mark<meta content="text/html; charset=utf-8" http-equiv="CONTENT-TYPE" /><title></title><meta content="OpenOffice.org 2.0 (Unix)" name="GENERATOR" /><meta content="gavrilov" name="AUTHOR" /><meta content="20110314;9335600" name="CREATED" /><meta content="gavrilov" name="CHANGEDBY" /><meta content="20110314;9564900" name="CHANGED" />
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<p style="margin-bottom: 0in;">You asking about this (?):
</p>
<p style="margin-bottom: 0in;">According to ffamber99.atp:</p>
<p style="margin-bottom: 0in;">amber99_34 14.01000 N sp2
nitrogen in amide groups</p>
<p style="margin-bottom: 0in;">amber99_39 14.01000 N3 sp3 N
for charged amino groups (Lys, etc)</p>
<p style="margin-bottom: 0in;">
</p>
<p style="margin-bottom: 0in;">If I don't mix, “N” is used in
peptide bond in amber99 and “N3” is used in Lys side chain. That
is why I didn't use backbone peptide.</p></div></div></blockquote><br />N3 is used in a quaternary amine. N is used in an amide. Atom types are related to the chemical functional group they are *now* in, not what they were before a notional peptide condensation. You have an amide, and the nitrogen in it cannot be protonated. I said that in an email a fortnight ago. Use normal peptide parameters.<br /><br /><blockquote cite="mid:AANLkTinGjZ4-Su-TvmUsBOt1jRc2gFzZdKKC37Eu6gAy@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div dir="ltr"><p style="margin-bottom: 0in;"></p>
<p style="margin-bottom: 0in;"><b>[atoms] and [bonds] section for LYQ
and GLQ in topol.top </b><br /><br />
</p>
<p style="margin-bottom: 0in;">[ atoms ]</p>
<p style="margin-bottom: 0in;">; nr type resnr residue atom
cgnr charge mass typeB chargeB massB</p>
<p style="margin-bottom: 0in;"> 750 amber99_34 48 LYQ N
748 -0.4157 14.01 ; qtot -5.416</p>
<p style="margin-bottom: 0in;"> 751 amber99_17 48 LYQ H
749 0.2719 1.008 ; qtot -5.144</p>
<p style="margin-bottom: 0in;"> 752 amber99_11 48 LYQ CA
750 -0.07206 12.01 ; qtot -5.216</p>
<p style="margin-bottom: 0in;"> 753 amber99_19 48 LYQ HA
751 0.0994 1.008 ; qtot -5.116</p>
<p style="margin-bottom: 0in;"> 754 amber99_11 48 LYQ CB
752 -0.04845 12.01 ; qtot -5.165</p>
<p style="margin-bottom: 0in;"> 755 amber99_18 48 LYQ HB1
753 0.034 1.008 ; qtot -5.131</p>
<p style="margin-bottom: 0in;"> 756 amber99_18 48 LYQ HB2
754 0.034 1.008 ; qtot -5.097</p>
<p style="margin-bottom: 0in;"> 757 amber99_11 48 LYQ CG
755 0.06612 12.01 ; qtot -5.031</p>
<p style="margin-bottom: 0in;"> 758 amber99_18 48 LYQ HG1
756 0.01041 1.008 ; qtot -5.02</p>
<p style="margin-bottom: 0in;"> 759 amber99_18 48 LYQ HG2
757 0.01041 1.008 ; qtot -5.01</p>
<p style="margin-bottom: 0in;"> 760 amber99_11 48 LYQ CD
758 -0.03768 12.01 ; qtot -5.048</p>
<p style="margin-bottom: 0in;"> 761 amber99_18 48 LYQ HD1
759 0.01155 1.008 ; qtot -5.036</p>
<p style="margin-bottom: 0in;"> 762 amber99_18 48 LYQ HD2
760 0.01155 1.008 ; qtot -5.025</p>
<p style="margin-bottom: 0in;"> 763 amber99_11 48 LYQ CE
761 0.32604 12.01 ; qtot -4.699</p>
<p style="margin-bottom: 0in;"> 764 amber99_28 48 LYQ HE1
762 -0.03358 1.008 ; qtot -4.732</p>
<p style="margin-bottom: 0in;"> 765 amber99_28 48 LYQ HE2
763 -0.03358 1.008 ; qtot -4.766</p>
<p style="margin-bottom: 0in;"> 766 amber99_39 48 LYQ NZ
764 -1.03581 14.01 ; qtot -5.801</p>
<p style="margin-bottom: 0in;"> 767 amber99_17 48 LYQ HZ1
765 0.38604 1.008 ; qtot -5.415</p>
<p style="margin-bottom: 0in;"> 768 amber99_17 48 LYQ HZ2
766 0.38604 1.008 ; qtot -5.029</p></div></div></blockquote><br />Atom 766 is bound to two carbon atoms and two hydrogen atoms. There is no such thing as a quaternary amide nitrogen, and certainly AMBER does not have parameters for it.<br /><br /><blockquote cite="mid:AANLkTinGjZ4-Su-TvmUsBOt1jRc2gFzZdKKC37Eu6gAy@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div dir="ltr"><p style="margin-bottom: 0in;"></p>
<p style="margin-bottom: 0in;"> 769 amber99_2 48 LYQ C
767 0.5973 12.01 ; qtot -4.432</p>
<p style="margin-bottom: 0in;"> 770 amber99_41 48 LYQ O
768 -0.5679 16 ; qtot -5</p>
<p style="margin-bottom: 0in;"><br />
</p>
<p style="margin-bottom: 0in;"><br />
</p>
<p style="margin-bottom: 0in;"> 2440 amber99_34 152 GLQ N
2438 -0.4157 14.01 ; qtot -12.42</p>
<p style="margin-bottom: 0in;"> 2441 amber99_17 152 GLQ H
2439 0.2719 1.008 ; qtot -12.14</p>
<p style="margin-bottom: 0in;"> 2442 amber99_11 152 GLQ CA
2440 -0.0252 12.01 ; qtot -12.17</p>
<p style="margin-bottom: 0in;"> 2443 amber99_19 152 GLQ HA1
2441 0.0698 1.008 ; qtot -12.1</p>
<p style="margin-bottom: 0in;"> 2444 amber99_19 152 GLQ HA2
2442 0.0698 1.008 ; qtot -12.03</p>
<p style="margin-bottom: 0in;"> 2445 amber99_2 152 GLQ C
2443 0.5973 12.01 ; qtot -11.43</p>
<p style="margin-bottom: 0in;"> 2446 amber99_41 152 GLQ O
2444 -0.5679 16 ; qtot -12</p>
<p style="margin-bottom: 0in;"><br />
</p>
<p style="margin-bottom: 0in;"><br />
</p>
<p style="margin-bottom: 0in;">[ bonds ]</p>
<p style="margin-bottom: 0in;">; ai aj funct c0
c1 c2 c3</p>
<p style="margin-bottom: 0in;"> 750 751 1
</p>
<p style="margin-bottom: 0in;"> 750 752 1
</p>
<p style="margin-bottom: 0in;"> 752 753 1
</p>
<p style="margin-bottom: 0in;"> 752 754 1
</p>
<p style="margin-bottom: 0in;"> 752 769 1
</p>
<p style="margin-bottom: 0in;"> 754 755 1
</p>
<p style="margin-bottom: 0in;"> 754 756 1
</p>
<p style="margin-bottom: 0in;"> 754 757 1
</p>
<p style="margin-bottom: 0in;"> 757 758 1
</p>
<p style="margin-bottom: 0in;"> 757 759 1
</p>
<p style="margin-bottom: 0in;"> 757 760 1
</p>
<p style="margin-bottom: 0in;"> 760 761 1
</p>
<p style="margin-bottom: 0in;"> 760 762 1
</p>
<p style="margin-bottom: 0in;"> 760 763 1
</p>
<p style="margin-bottom: 0in;"> 763 764 1
</p>
<p style="margin-bottom: 0in;"> 763 765 1
</p>
<p style="margin-bottom: 0in;"> 763 766 1
</p>
<p style="margin-bottom: 0in;"> 766 767 1
</p>
<p style="margin-bottom: 0in;"> 766 768 1
</p>
<p style="margin-bottom: 0in;"> 766 2445 1
</p></div></div></blockquote><br />OK, you have the N-C bond for the peptide link.<br /><br /><blockquote cite="mid:AANLkTinGjZ4-Su-TvmUsBOt1jRc2gFzZdKKC37Eu6gAy@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div dir="ltr"><p style="margin-bottom: 0in;"></p>
<p style="margin-bottom: 0in;"> 769 770 1
</p>
<p style="margin-bottom: 0in;"> 769 771 1
</p>
<p style="margin-bottom: 0in;"><br />
</p>
<p style="margin-bottom: 0in;"><br />
</p>
<p style="margin-bottom: 0in;"> 2440 2441 1
</p>
<p style="margin-bottom: 0in;"> 2440 2442 1
</p>
<p style="margin-bottom: 0in;"> 2442 2443 1
</p>
<p style="margin-bottom: 0in;"> 2442 2444 1
</p>
<p style="margin-bottom: 0in;"> 2442 2445 1
</p>
<p style="margin-bottom: 0in;"> 2445 2446 1
</p></div></div></blockquote><br />Does 2445 make any other bonds? If not, how did you handle the chain termination?<br /><br />Mark