Hello, I want to apply restrain on ligand in GROMACS5, so I build it with genres and include in topology and define in mdp. But I think it did not work., because ligand move a lot, even with 100000 restrain. I am not sure that the ligand have restrain, how can I be sure? Is applying restrain same in version 5 of GROMACS?
Dear Krishnendu,
Thank you for your answer. But I am not sure that I got. You mean after em, do different restrains (force constant) on protein in 8 short simulation?
But I have problem with ligand that move while there is strong restrains.
Hi Zohrah,
Yes, applying restraints is same in GROMACS 5.0. Did you put the include term right under the ligand block referring to its topology? Did you check that names are correct and matching at both positions (in *.top and *.mdp) in files? There might be something that you are missing that leads to failing the application of restraints.
HTH,
Ayaz
Hi,thank you Mohammad.
But if the ligand restrain is after protein restrain e.i , it can not apply this restrain on ligand?
Hi Zohreh,
Nope, the block sequence is a kind of strict, like you can not put ligand restraint file after protein. If you did this, then restraints have been applied on the protein atoms, not the ligand.
You need to do something like this:
; Include chain topologies
#include "topol_ligand_chain.itp"
#ifdef POSRES
#include "posre_ligand_chain.itp"
#endif
HTH,
Ayaz
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