[gmx-users] Getting ligand's topology

[RAHUL SURESH]

I cannot assist you much with the description of your ligand. But what I
have seen is, ring with N shows maximum penalities in most cases.

When you optimise with mp2, the structure shows no much changes.
So penalty is same most time.

Try to download file from Zinc15 database which is most preferred file
 cgenff. Still the penalty may exist in cse of N in ring. It could be
optimised using ffTK. Again I find your structure is pretty big which will
be time consuming. Or you have to adapt divide and conquer method, which is
going to be complicated. So it’s your wise choice always. Maybe others,
especially Dr. Justin or Dr. Mark could give you a better soln.

Thank you

On Sat, 18 Aug 2018 at 10:17 PM, Mahdi Sobati Nezhad <
mahdisobatinezhad at gmail.com> wrote:

> 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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-- 
*Regards,*
*Rahul *