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gql119

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[交流] 【讨论】用syby分子对接求吉布斯自由能已有8人参与

用sybyl分子对接小分子和生物大分子后，如何求它们的吉布斯自由能？或软件上如何操作才能得到这个值？l

[ Last edited by gql119 on 2010-4-25 at 11:11 ]

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1楼 2010-04-25 11:09:59

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SYBYL 能量计算

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SYBYLTutorial: Minimizing small molecules
The material presented in this tutorial is based primarily on the material given in the 'Tutorial Manual' of the SYBYL software package. Preface This tutorial higlights the general capabilities of the minimizer. You will use the atropine molecule sketched in the previous tutorial to illustrate some of the features of MAXIMIN2, SYBYL's energy minimizer. From the raw model, two different conformations are optimized, and the results are compared with the conformation found from a crystallographic analyses (E.Kussather & J.Haase, Acta Crystallogr.,Sect.B, 28, 2896 (1972)). After this tutorial you will be able to, a.o.:

* Measure geometrical features
* Modify a model geometrically
* Setup and perform energy calculations
* Setup and perform optimizations
* Superimpose structures

Clearing work areas

* Clear all the molecule and display areas if necessary. BUILD/EDIT >>> ZAP (DELETE) MOLECULE
   If there is more than one molecule on the screen, click ALL, then OK to wipe them all.
* RESET your screen if necessary. Use the RESET gadget to reset EVERYTHING
   Use the DISPLAY OPTIONS to reset to FULL screen mode.
* Delete backgrounds, if any: VIEW >>> DELETE ALL BACKGROUNDS

Read molecule 'atropine'

* Read a raw model of atropine into work area M1: From the FILE >>> READ... menu,
   type ta_demo:atropine_raw.mol2 in the 'File to read' area. (Press OK) Alternatively, you may use your own sketch model of atropine. In that case, choose the name from the 'Files' box. Do make sure 'atropine' is read into workarea M1.

Setting up and submitting the minimization

* Specify the energy parameters: COMPUTE >>> MINIMIZE...
   Press the MODIFY... button.
   Set the appropriate options to make the Energy dialog box looks like the one in Fig.8. In particular:
   - Select TRIPOS in the Force Field option menu,
   - Select GASTEIGER-HUCKEL in the Charges option menu.
   Press OK.

Fig.8 Energy dialog box
* The Minimize dialog box reappears. Set some of the minimization options using the Minimize Details dialog box:。。。。。。
* http://www.cmbi.kun.nl/samsam/tu ... l/tut.minim001.html