[gmx-users] QM/MM

[Antonio Sergio Kimus Braz]

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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