<div dir="ltr">Dear, Mark<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8"><title></title><meta name="GENERATOR" content="OpenOffice.org 2.0 (Unix)"><meta name="AUTHOR" content="gavrilov"><meta name="CREATED" content="20110314;9335600"><meta name="CHANGEDBY" content="gavrilov"><meta name="CHANGED" content="20110314;9564900">
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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>
<p style="margin-bottom: 0in;"><br>
</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>
<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>
<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>
<br>-- <br><div dir="ltr"><p style="margin-bottom: 0in;">Sincerely,</p>
<p style="margin-bottom: 0in;">Yulian Gavrilov
</p></div><br>
</div>