[gmx-users] restrain ligand in free energy.
hoangtung9597 at gmail.com
Wed Aug 29 16:19:07 CEST 2018
Tks for your reply. But this restrain -fc 1000 1000 1000 i ready know it is using for nvt npt . But for md run. They don't use that restrain. Because i am going to calculate free energy. Dental G restrain on .
-------- Tin nhắn gốc --------Từ: Bratin Kumar Das <177cy500.bratin at nitk.edu.in> Ngày: 29/08/2018 19:05 (GMT+07:00) Đến: gmx-users at gromacs.org Chủ đề: Re: [gmx-users] restrain ligand in free energy.
Gromacs has genrestr programme...In protein-ligand complex tutorial
it is mentioned(how to restrain ligand)
The command is
gmx genrestr -f ligand.gro -o ligand_posre.itp -fc 1000 1000 1000
After that you need to include in the main topology
On Wed 29 Aug, 2018, 12:37 PM Tùng Hoàng, <hoangtung9597 at gmail.com> wrote:
> Hello everyone,
> i am trying to calculate free energy for complex protein-ligand. but in
> tutorial it just have methane in water. So i find this
> but the problem is i don know how to restrain this ligand.
> in file complex.top i see that intramolecular - interaction , bond, angle ,
> diheral. and in .mdp file i see bonds_lambda increase. I wonder how i can
> restrain like this . where i can find intramolecular -interaction/....
> Thank you for your help.
> Hoàng Tùng / student
> hoangtung9597 at gmail.com / +(84) 0928 478 789
> University of Medicine and Pharmacy I Ho Chi Minh City
> 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
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