[gmx-users] Getting ligand's topology

[Mahdi Sobati Nezhad]

Thanks for your help.
my ligand is three rings that connects with a carbon and this rings have
Nitrogen, oxygen, sulfur, carbon and Chlor...
And high penaltys are just for that ring that contains Nitrogen, carbon and
sulfur
And so on my choice is just using ffTK?!


On Sat, 18 Aug 2018 21:05 RAHUL SURESH, <drrahulsuresh at gmail.com> wrote:

> Hi.
>
> To resolve the penalties are bit complicated. Tools like ffTK can help you
> do it. But output from ffTK is as in charmm and henceforth it take
> additional work ( was difficult for me ) to modify it to Gromacs acceptable
> format.
>
> I personally don’t appreciate this method as it is very time consuming if
> your structure is big and having penalties in dihedrals which again make it
> complicated.
> Thank you
>
> On Sat, 18 Aug 2018 at 7:02 PM, Mahdi Sobati Nezhad <
> mahdisobatinezhad at gmail.com> wrote:
>
> > Hi
> > I'm a begginer in taking ligand's topology from CGENFF and my '.str' file
> > have some high penalty numbers. What I can do?!
> > And how I can do validation and optimization?!
> > I read the FAQ in its server but I don't understand!!!
> > Thanks
> > --
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> *Regards,*
> *Rahul *
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