[gmx-users] Regarding Fatal error

[Justin Lemkul]

On 10/5/16 2:30 PM, Kamal Chaudhary wrote:
> Dear All,
>
> when i run grompp i got this error
>
> gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tp
>
>
> Fatal error:
> Group Protein 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.
>
> my topol.top contain these informations
>
> [ molecules ]
> ; Compound        #mols
> DNA_chain_E         1
> SOL         5564
> CL               8
>
> and this is the nvt.mdp entry
>
> ; Temperature coupling is on
> tcoupl        = V-rescale                ; modified Berendsen thermostat
> tc-grps        = Protein Non-Protein    ; two coupling groups - more
> accurate

If your system has no protein, you can't use the "Protein" default group.  You 
need to specify suitable groups based on the contents of your system.

-Justin

> tau_t        = 0.1      0.1           ; time constant, in ps
> ref_t        = 300       300           ; reference temperature, one for
> each group, in K
> ; Pressure coupling is off
> pcoupl        = no         ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc        = xyz            ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = yes        ; assign velocities from Maxwell distribution
> gen_temp    = 300        ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
>

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

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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