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

[Justin Lemkul]

On 10/29/15 6:45 AM, Nikhil Maroli wrote:
> 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
>

Protein_LIG suggests a merged protein and ligand group.  You need to invoke 
make_ndx to create a group that has such contents.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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