[gmx-users] Group Protein_LIG referenced in the .mdp file was not found in the index file.:Protein-Ligand MD
jalemkul at vt.edu
Thu Oct 29 19:12:58 CET 2015
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
> 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
> 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 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
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