[gmx-users] probelm of using amber force field

[Justin A. Lemkul]

fancy2012 wrote:
> Dear GMX users,
>  
> I have a question about running MD simulation using amber force 
> field. It is easy to prepare the top and gro files of protein with amber 
> force field, but how should I prepare the itp and gro files of small 
> molecules  with GAFF force field? I know the program ANTECHAMBER and 
> tleap can generate the some molecule's topology and coordinate. Could 
> someone give me some hints? Thanks very much in advance!

http://code.google.com/p/acpype/ is one common approach.

-Justin

>  
> --
> 
> _Best wishes,_
> 
> _Qinghua Liao_
> 
> _Ph.D student of Tianjin University, China_
> 

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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