[gmx-users] Getting ligand's topology

RAHUL SURESH drrahulsuresh at gmail.com
Sat Aug 18 18:34:42 CEST 2018


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

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
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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