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标题: Request advice about software for conformational search for organic molecules [打印本页]

作者
Author: mekelleche 时间: 2020-6-27 07:38
标题: Request advice about software for conformational search for organic molecules
Hi guys,
Can you advise me about a good and free software that can perform a conformational search (Molecular Mechanics), because i found a good one (conflex software), but it's a little bit expansive.

作者
Author: wangzhe 时间: 2020-6-27 08:30
In our lab, we use Pcmodel 10, it is a free software developed by the same company with GMMX module in GaussView. It also has same functions with GMMX. You can get more information from this page http://www.serenasoft.com/.

作者
Author: snljty 时间: 2020-6-27 09:06
Molclus
http://www.keinsci.com/research/molclus.html
It can flexible invoke Gaussian, ORCA, MOPAC, GFN-xtb and Open Babel to perform a construction or conformation search at any level literally conveniently.

Btw, what is the size of your molecule? MM-level methods could not even qualitatively confirm that you got the lowest energy conformation. A QM-level step may be necessary, as long as you can afford the computing cost.

作者
Author: sobereva 时间: 2020-6-27 17:04
MM is rarely useful if you need to obtain lowest conformer and qualitatively reasonable Boltzmann weights. See Int J Quantum Chem., 118, e25512 (2018)
MM at most can be used to sample potential energy surface, while further optimizations and energy calculations must be carried out at DFT level or better, as illustrated in my conformation search tutorial articles using molclus:
使用Molclus结合xtb做的动力学模拟对瑞德西韦(Remdesivir)做构象搜索
http://bbs.keinsci.com/thread-16255-1-1.html
gentor：扫描方式做分子构象搜索的便捷工具
http://bbs.keinsci.com/thread-2388-1-1.html

Molclus is freely available and quite flexible, any level supported by Gaussian, ORCA, MOPAC, Openbabel, xtb can be combined into conformation search process, and molclus provides very convenient tool to generate initial geometries, sort optimized geometries and remove duplicates.

作者
Author: mekelleche 时间: 2020-6-27 18:27
Thank you very much guys for your good replies.
Dear wangzhe, GMMX is very good, but unfortunately, i can't afford the price.
Dear snljty, i work with molecule about 30 atoms.
Dear Sobereva, molclus is good and free, but i'm looking for using the MMFF94. Does molclus support it ?

作者
Author: wangzhe 时间: 2020-6-27 20:11

mekelleche 发表于 2020-6-27 19:27
Thank you very much guys for your good replies.
Dear wangzhe, GMMX is very good, but unfortunately, ...

Pcmodel 10 is free, and it it same software with GMMX. You can get this point from the icon. If you want to use GMMX but can not afford the money, you can try Pcmodel, they are totally same. And also, MM is supported.

作者
Author: mekelleche 时间: 2020-6-27 20:52
Thank you very much Dear wangzhe.

作者
Author: sobereva 时间: 2020-6-29 01:33

mekelleche 发表于 2020-6-27 18:27
Thank you very much guys for your good replies.
Dear wangzhe, GMMX is very good, but unfortunately, ...

Using molclus in combination with the freely available OpenBabel, you can use MMFF94 to perform conformation search.
However, a much better choice is using molclus in combination with xtb, the GFN-xTB supported by xtb is extremely fast and the accuracy is significantly better than MMFF94. For conformation search of a molecule containing ~30 atoms, I do not believe this is any reason to still use the very old MMFF94.

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