[gmx-users] QM/MM

[Pradip Kumar Biswas]

Which QM method are you using?

pb.

On Aug 2, 2006, at 9:50 AM, Antonio Sergio Kimus Braz wrote:

> 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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--
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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