Dear Jorden,
Many thanks for your suggestions. I solved the index file problem as I created two groups namely Protein_Zn_NAD and the other being Na_Water. But when i ran NVT equilibration, the Zn ion again got displaced far away from its original position. I cannot figure out how can i constrain the Zn ion? I guess something is wrong in the topology file. I have included the last few lines of my topology file. Please have a look whenever you are free and correct me if something is mistakenly wrong. Thanks for your time and help.
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include Position restraint file
#ifdef POSRES
#include "posre_zn.itp"
#endif
; Include ligand topology
#include "nad.itp"
; Ligand position restraints
#ifdef POSRES_LIG
#include "posre_nad.itp"
#endif
; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./charmm36-mar2019.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
ZN 1
NAD 1
SOL 12908
NA 4
With kind regards,
Amit
11.10.2019, 18:10, "Jorden Cabal" <jordenca...@gmail.com>:
Dear Amit,
--
Please check if the Zn ion is included in both the groups declared for
temperature coupling. If you notice that it is is included, you can simply
create a group of all the atoms which is not in "Protein_NAD" group. You
can do this by using "!group_number" as far as I remember. Then try this,
it should work. Please mail if the problem persists.
Thank you and all the best.
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