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<p class="western" style="margin-bottom: 0cm;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">H<span style="font-weight: bold;">i
all</span></font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">I
need help for QM/MM </font></font>
</p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">I
believ that my problem is interface between QMatoms Mmatoms...</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">I
try simulate a metalloprotease </font></font>
</p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">I
use gromos96 53a6 forcefield </font></font>
</p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">and
make distance restraint for Zn – 3x (NE2) HIS for simulate ZN 3 x
HIS interaction</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">and
try make o hybrid QM/MM method for this simulation</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">I
define the atoms for QM</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">HIS
141 HIS 145 HIS 151</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">ZN
201</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i><span style="font-weight: bold;">HOH
221 HOH 269 HOH 270</span> </i></font></font></font>
</p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"> QMatoms are<br>
</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1466
1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1504
</i></font></font></font>
</p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1505
1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1562 1563
</i></font></font></font>
</p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1564
1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 2063 2121 2122
</i></font></font></font>
</p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>2123
2265 2266 2267 2268 2269 2270</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><br>
</p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">this
is good size region for QM ? Its big ? ... or small ?</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">I
believ that my problem is interface between QMatoms Mmatoms</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">I
insert in .top files this parameters :<br>
<br>
</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"></p><p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">
<i>[
virtual_sites2 ]</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>LA
1466 1464 1 0.65</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>LA
1478 1480 1 0.65</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>LA
1504 1502 1 0.65</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>LA
1516 1518 1 0.65</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>LA
1562 1560 1 0.65</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>LA
1574 1576 1 0.65<br>
<br>
</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>[
constraints ]</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1466
1464 2 0.135</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1478
1480 2 0.135</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1504
1502 2 0.135</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1516
1518 2 0.135</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1562
1560 2 0.135</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font color="#000000"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><i>1574
1576 2 0.135</i></font></font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><br>
</p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch" size="6"><font style="font-size: 8pt;">and
in [ bonds ] I replace the numeric values ob QMatoms bonds for 5 ...</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch" size="6"><font style="font-size: 8pt;">exemple :</font></font><span style="font-weight: bold;"></span></p>
<font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1"><font size="4"></font></font></font><p class="western" style="margin-bottom: 0cm;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">
<br>
</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">[
bonds ]</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">...</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1504
1505 5 gb_2</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1504
1506 5 gb_21</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1506
1507 5 gb_27</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1506
1516 5 gb_27</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1507
1508 5 gb_27</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1508
1509 5 gb_10</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1508
1511 5 gb_10</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1509
1510 5 gb_2</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1509
1513 5 gb_10</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1511
1512 5 gb_3</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1511
1515 5 gb_10</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1513
1514 5 gb_3</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1513
1515 5 gb_10</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"> <font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">1516
1517 5 gb_5</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">...</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><br>
</p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font size="4"><br>
</font>
</p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch" size="4"><font style="font-size: 8pt;">and
replace name of HISA (in HIS 141 HIS 145 and HIS 151) for CYX em top
an gro file</font></font></p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font size="4"><br>
</font>
</p>
<p class="western" style="margin-bottom: 0cm; font-weight: bold;" align="justify"><font face="Courier 10 Pitch" size="4"><font style="font-size: 8pt;">I
create to index.ndx for QMatoms
</font></font>
</p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font face="Courier 10 Pitch" size="4"><font style="font-size: 8pt;"><br>thank
you very much</font></font></p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><br>
</p>
<p class="western" style="margin-bottom: 0cm;" align="justify"><font face="Courier 10 Pitch"><font style="font-size: 8pt;" size="1">Antonio
Sergio Kimus Braz</font></font></p>
<br>
<br>