176 related articles for article (PubMed ID: 12820132)
1. A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems.
Loferer MJ; Loeffler HH; Liedl KR
J Comput Chem; 2003 Jul; 24(10):1240-9. PubMed ID: 12820132
[TBL] [Abstract][Full Text] [Related]
2. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
Lu Z; Yang W
J Chem Phys; 2004 Jul; 121(1):89-100. PubMed ID: 15260525
[TBL] [Abstract][Full Text] [Related]
3. Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex.
Rungrotmongkol T; Mulholland AJ; Hannongbua S
J Mol Graph Model; 2007 Jul; 26(1):1-13. PubMed ID: 17046299
[TBL] [Abstract][Full Text] [Related]
4. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
Hu H; Lu Z; Parks JM; Burger SK; Yang W
J Chem Phys; 2008 Jan; 128(3):034105. PubMed ID: 18205486
[TBL] [Abstract][Full Text] [Related]
5. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
Riccardi D; Schaefer P; Cui Q
J Phys Chem B; 2005 Sep; 109(37):17715-33. PubMed ID: 16853267
[TBL] [Abstract][Full Text] [Related]
6. Combining quantum wavepacket ab initio molecular dynamics with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical valence bond theory.
Sumner I; Iyengar SS
J Chem Phys; 2008 Aug; 129(5):054109. PubMed ID: 18698890
[TBL] [Abstract][Full Text] [Related]
7. The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.
Riahi S; Rowley CN
J Comput Chem; 2014 Oct; 35(28):2076-86. PubMed ID: 25178266
[TBL] [Abstract][Full Text] [Related]
8. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.
Lin H; Truhlar DG
J Phys Chem A; 2005 May; 109(17):3991-4004. PubMed ID: 16833721
[TBL] [Abstract][Full Text] [Related]
9. The QM-MM interface for CHARMM-deMon.
Lev B; Zhang R; de la Lande A; Salahub D; Noskov SY
J Comput Chem; 2010 Apr; 31(5):1015-23. PubMed ID: 20027641
[TBL] [Abstract][Full Text] [Related]
10. Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping.
Xiang Y; Warshel A
J Phys Chem B; 2008 Jan; 112(3):1007-15. PubMed ID: 18166038
[TBL] [Abstract][Full Text] [Related]
11. Prediction and rationalization of protein pKa values using QM and QM/MM methods.
Jensen JH; Li H; Robertson AD; Molina PA
J Phys Chem A; 2005 Aug; 109(30):6634-43. PubMed ID: 16834015
[TBL] [Abstract][Full Text] [Related]
12. Computational methods for the study of enzymic reaction mechanisms III: a perturbation plus QM/MM approach for calculating relative free energies of protonation.
Cummins PL; Gready JE
J Comput Chem; 2005 Apr; 26(6):561-8. PubMed ID: 15726569
[TBL] [Abstract][Full Text] [Related]
13. Testing high-level QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase.
van der Kamp MW; Zurek J; Manby FR; Harvey JN; Mulholland AJ
J Phys Chem B; 2010 Sep; 114(34):11303-14. PubMed ID: 20690673
[TBL] [Abstract][Full Text] [Related]
14. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.
Liu H; Lu Z; Cisneros GA; Yang W
J Chem Phys; 2004 Jul; 121(2):697-706. PubMed ID: 15260596
[TBL] [Abstract][Full Text] [Related]
15. An efficient method for the calculation of quantum mechanics/molecular mechanics free energies.
Woods CJ; Manby FR; Mulholland AJ
J Chem Phys; 2008 Jan; 128(1):014109. PubMed ID: 18190187
[TBL] [Abstract][Full Text] [Related]
16. Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach.
He X; Wang B; Merz KM
J Phys Chem B; 2009 Jul; 113(30):10380-8. PubMed ID: 19575540
[TBL] [Abstract][Full Text] [Related]
17. Development and application of a hybrid method involving interpolation and ab initio calculations for the determination of transition states.
Goodrow A; Bell AT; Head-Gordon M
J Chem Phys; 2008 Nov; 129(17):174109. PubMed ID: 19045335
[TBL] [Abstract][Full Text] [Related]
18. Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method.
Ferré N; Assfeld X; Rivail JL
J Comput Chem; 2002 Apr; 23(6):610-24. PubMed ID: 11939595
[TBL] [Abstract][Full Text] [Related]
19. Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: comparison of semiempirical, ab initio, and density functional results.
Linnanto J; Korppi-Tommola J
J Comput Chem; 2004 Jan; 25(1):123-38. PubMed ID: 14635000
[TBL] [Abstract][Full Text] [Related]
20. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.
Rosta E; Klähn M; Warshel A
J Phys Chem B; 2006 Feb; 110(6):2934-41. PubMed ID: 16471904
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
