pb.
On Aug 2, 2006, at 9:50 AM, Antonio Sergio Kimus Braz wrote:
<x-tad-smaller>H</x-tad-smaller><x-tad-smaller>i all</x-tad-smaller>--
<x-tad-smaller>I need help for QM/MM</x-tad-smaller>
<x-tad-smaller>I believ that my problem is interface between QMatoms Mmatoms...</x-tad-smaller>
<x-tad-smaller>I try simulate a metalloprotease</x-tad-smaller>
<x-tad-smaller>I use gromos96 53a6 forcefield</x-tad-smaller>
<x-tad-smaller>and make distance restraint for Zn – 3x (NE2) HIS for simulate ZN 3 x HIS interaction</x-tad-smaller>
<x-tad-smaller>and try make o hybrid QM/MM method for this simulation</x-tad-smaller>
<x-tad-smaller>I define the atoms for QM</x-tad-smaller>
<x-tad-smaller>HIS 141 HIS 145 HIS 151</x-tad-smaller>
<x-tad-smaller>ZN 201</x-tad-smaller>
<x-tad-smaller>HOH 221 HOH 269 HOH 270</x-tad-smaller><x-tad-smaller> </x-tad-smaller>
<x-tad-smaller> QMatoms are</x-tad-smaller>
<x-tad-smaller>1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1504</x-tad-smaller>
<x-tad-smaller>1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1562 1563</x-tad-smaller>
<x-tad-smaller>1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 2063 2121 2122</x-tad-smaller>
<x-tad-smaller>2123 2265 2266 2267 2268 2269 2270</x-tad-smaller>
<x-tad-smaller>this is good size region for QM ? Its big ? ... or small ?</x-tad-smaller>
<x-tad-smaller>I believ that my problem is interface between QMatoms Mmatoms</x-tad-smaller>
<x-tad-smaller>I insert in .top files this parameters :</x-tad-smaller>
<x-tad-smaller>[ virtual_sites2 ]</x-tad-smaller>
<x-tad-smaller>LA 1466 1464 1 0.65</x-tad-smaller>
<x-tad-smaller>LA 1478 1480 1 0.65</x-tad-smaller>
<x-tad-smaller>LA 1504 1502 1 0.65</x-tad-smaller>
<x-tad-smaller>LA 1516 1518 1 0.65</x-tad-smaller>
<x-tad-smaller>LA 1562 1560 1 0.65</x-tad-smaller>
<x-tad-smaller>LA 1574 1576 1 0.65</x-tad-smaller>
<x-tad-smaller>[ constraints ]</x-tad-smaller>
<x-tad-smaller>1466 1464 2 0.135</x-tad-smaller>
<x-tad-smaller>1478 1480 2 0.135</x-tad-smaller>
<x-tad-smaller>1504 1502 2 0.135</x-tad-smaller>
<x-tad-smaller>1516 1518 2 0.135</x-tad-smaller>
<x-tad-smaller>1562 1560 2 0.135</x-tad-smaller>
<x-tad-smaller>1574 1576 2 0.135</x-tad-smaller>
<x-tad-smaller>and in [ bonds ] I replace the numeric values ob QMatoms bonds for 5 ...</x-tad-smaller>
<x-tad-smaller>exemple :</x-tad-smaller>
<x-tad-smaller>[ bonds ]</x-tad-smaller>
<x-tad-smaller>...</x-tad-smaller>
<x-tad-smaller>1504 1505 5 gb_2</x-tad-smaller>
<x-tad-smaller>1504 1506 5 gb_21</x-tad-smaller>
<x-tad-smaller>1506 1507 5 gb_27</x-tad-smaller>
<x-tad-smaller>1506 1516 5 gb_27</x-tad-smaller>
<x-tad-smaller>1507 1508 5 gb_27</x-tad-smaller>
<x-tad-smaller>1508 1509 5 gb_10</x-tad-smaller>
<x-tad-smaller>1508 1511 5 gb_10</x-tad-smaller>
<x-tad-smaller>1509 1510 5 gb_2</x-tad-smaller>
<x-tad-smaller>1509 1513 5 gb_10</x-tad-smaller>
<x-tad-smaller>1511 1512 5 gb_3</x-tad-smaller>
<x-tad-smaller>1511 1515 5 gb_10</x-tad-smaller>
<x-tad-smaller>1513 1514 5 gb_3</x-tad-smaller>
<x-tad-smaller>1513 1515 5 gb_10</x-tad-smaller>
<x-tad-smaller>1516 1517 5 gb_5</x-tad-smaller>
<x-tad-smaller>...</x-tad-smaller>
<x-tad-smaller>and replace name of HISA (in HIS 141 HIS 145 and HIS 151) for CYX em top an gro file</x-tad-smaller>
<x-tad-smaller>I create to index.ndx for QMatoms </x-tad-smaller>
<x-tad-smaller>thank you very much</x-tad-smaller>
<x-tad-smaller>Antonio Sergio Kimus Braz</x-tad-smaller>
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Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
http://comppsi.csuohio.edu/groups/people/biswas.html
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