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smutao禁蟲 (著名寫手)
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[smutao文集-自編教程]如何快速構(gòu)建單鏈Polymer模型？ 已有1人參與
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最近做了一點和polymer有關(guān)的工作，想到了一個快速構(gòu)建單鏈polymer的方式。 希望對大家有幫助。 Sometimes, when we need to do some research on polymers using the MD simulation methods, we have to construct models of them first. It is a common way to construct such models using commercial software packages such as Material Studio, Discovery Studio and so forth. But what can we do without them? The main tool we need to construct such models is Open Babel. Following is the protocol: 1. Get the structure information of the polymer you study(usually the 2D structure); 2. Draw a short sample of the polymer in Chemdraw saving as ".cdx" file or 3D modeling software such as GaussView saving as ".mol2" file; 3. Using Open Babel to convert the ".cdx" or ".mol2" file into SMILES format; 4. Look at the SMILES string and learn how it is organized; 5. Write the SMILES string for the polymer you study; 6. Using Open Babel to convert the SMILES format into a ".mol2" file. So the raw model has been constructed. However, there are a little problems before using it for MD simulation. Firstly, there will be same atom names, and we have to adjust them to avoid conflicts. Secondly, no other problems found... :-) Enjoy! |
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2014-06-11 10:21:37, 93.36 K
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