[gmx-users] Group Protein_LIG referenced in the .mdp file was not found in the index file.:Protein-Ligand MD

Nikhil Maroli scinikhil at gmail.com
Thu Oct 29 11:45:42 CET 2015


Dear All,
i am following protein-Ligand tutorial for my protein and ligand .
when i run grompp i got this error


Group Protein_LIG referenced in the .mdp file was not found in the index
file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

in my index file contain LIG entry  and in nvt.mdp also
should i change index entry to something else?or my .mdp file?
i tried by changing to Non-protein or others but it didnt work


my topol.top contain these informations

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 1
SOL             18612
NA                  6


this is the .mdp entry

; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
*tc-grps     = Protein_LIG Water_and_ions *   ; two coupling groups - more
accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature, one
for each group, in K
; Pressure coupling


thanks
-- 
Ragards,
Nikhil Maroli


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