|
|
|
|
| LEADER |
01000caa a22002652c 4500 |
| 001 |
NLM202401782 |
| 003 |
DE-627 |
| 005 |
20250212030907.0 |
| 007 |
cr uuu---uuuuu |
| 008 |
231223s2011 xx |||||o 00| ||eng c |
| 024 |
7 |
|
|a 10.1002/jcc.21678
|2 doi
|
| 028 |
5 |
2 |
|a pubmed25n0675.xml
|
| 035 |
|
|
|a (DE-627)NLM202401782
|
| 035 |
|
|
|a (NLM)20949515
|
| 040 |
|
|
|a DE-627
|b ger
|c DE-627
|e rakwb
|
| 041 |
|
|
|a eng
|
| 100 |
1 |
|
|a Okamoto, Takuya
|e verfasserin
|4 aut
|
| 245 |
1 |
2 |
|a A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation
|
| 264 |
|
1 |
|c 2011
|
| 336 |
|
|
|a Text
|b txt
|2 rdacontent
|
| 337 |
|
|
|a ƒaComputermedien
|b c
|2 rdamedia
|
| 338 |
|
|
|a ƒa Online-Ressource
|b cr
|2 rdacarrier
|
| 500 |
|
|
|a Date Completed 15.06.2011
|
| 500 |
|
|
|a Date Revised 01.08.2012
|
| 500 |
|
|
|a published: Print-Electronic
|
| 500 |
|
|
|a CommentIn: J Comput Chem. 2012 Jul 15;33(19):1643-4. doi: 10.1002/jcc.23003. - PMID 22570199
|
| 500 |
|
|
|a Citation Status MEDLINE
|
| 520 |
|
|
|a Copyright © 2010 Wiley Periodicals, Inc.
|
| 520 |
|
|
|a For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER-GAUSSIAN interface (AG-IF), which can be one of the simplest architectures. In the AG-IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG-IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG-IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces
|
| 650 |
|
4 |
|a Journal Article
|
| 650 |
|
4 |
|a Research Support, Non-U.S. Gov't
|
| 700 |
1 |
|
|a Yamada, Kenta
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Koyano, Yoshiyuki
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Asada, Toshio
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Koga, Nobuaki
|e verfasserin
|4 aut
|
| 700 |
1 |
|
|a Nagaoka, Masataka
|e verfasserin
|4 aut
|
| 773 |
0 |
8 |
|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 32(2011), 5 vom: 15. Apr., Seite 932-42
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnas
|
| 773 |
1 |
8 |
|g volume:32
|g year:2011
|g number:5
|g day:15
|g month:04
|g pages:932-42
|
| 856 |
4 |
0 |
|u http://dx.doi.org/10.1002/jcc.21678
|3 Volltext
|
| 912 |
|
|
|a GBV_USEFLAG_A
|
| 912 |
|
|
|a SYSFLAG_A
|
| 912 |
|
|
|a GBV_NLM
|
| 912 |
|
|
|a GBV_ILN_350
|
| 951 |
|
|
|a AR
|
| 952 |
|
|
|d 32
|j 2011
|e 5
|b 15
|c 04
|h 932-42
|