Re: [gmx-users] Getting ligand's topology

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

Re: [gmx-users] Getting ligand's topology

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

Re: [gmx-users] Getting ligand's topology

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

[gmx-users] Getting ligand's topology

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 -- Gromacs Users mailing list * Please search the archive at