Optimizing force-field with AmberTools for small organic molecules in water

dr.bra... at gmail.com dr.bra... at gmail.com
Fri Dec 22 00:36:16 UTC 2017

Dear ALL,

I have problems with preparing system for ab initio molecular dynamic 
simulation of phenyletilamine (PEA). I need to do something similar to 
this: https://www.cp2k.org/exercises:2015_cecam_tutorial:urea but with PEA 
and pure AIMD, not QM/MM. I have issues with first part, to be more 
accurate I'm failing to reach the point where I can use files 
and Files/mol_solv.top 
<http://cp2k.org/static/exercises/2015_cecam_tutorial/UREA/Files/mol_solv.top> which 
are obtained with leap.  I've tried to follow all kind of tutorial on the 
web, but they are all connected to larger systems, such as protein ones. 
None of them is dealing with these small organic molecules such PEA.

I'd really appreciate if somebody could point me directions how to reach my 
goal since I',m beginner with these things. It does not have to be 
AmberTools software package to reach my goal to be clear.

Thanks in advance!!
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