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