[gmx-users] Regarding Umbrella sampling

[Justin Lemkul]

On 3/8/17 8:11 PM, Amir Zeb wrote:
> Hello gmx users,
>
> I want to calculate binding energy for a protein-ligand complex. Obviously,
> this is the very first time, I'm handling umbrella sampling, so I faced the
> following error.
>
> WARNING 2 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_ncoords' in parameter file
>
>
>
> WARNING 3 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_group1_name' in parameter file
>
>
>
> WARNING 4 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_group2_name' in parameter file
>
>
>
> WARNING 5 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_coord1_type' in parameter file
>
>
>
> WARNING 6 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_coord1_geometry' in parameter file
>
>
>
> WARNING 7 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_coord1_groups' in parameter file
>
>
>
> WARNING 8 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_coord1_dim' in parameter file
>
>
>
> WARNING 9 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_coord1_rate' in parameter file
>
>
>
> WARNING 10 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_coord1_k' in parameter file
>
>
>
> WARNING 11 [file pull.mdp, line 65]:
>   Unknown left-hand 'pull_coord1_start' in parameter file
>
>
>
> There was 1 note
>
> There were 11 warnings
>
>
> *The pull.mdp file is this one:*
>
> title       = Umbrella pulling simulation
> define      = -DPOSRES_NAD
> ; Run parameters
> integrator  = md
> dt          = 0.002
> tinit       = 0
> nsteps      = 250000    ; 500 ps
> nstcomm     = 10
> ; Output parameters
> nstxout     = 5000      ; every 10 ps
> nstvout     = 5000
> nstfout     = 500
> nstxtcout   = 500       ; every 1 ps
> nstenergy   = 500
> ; Bond parameters
> constraint_algorithm    = lincs
> constraints             = all-bonds
> continuation            = yes       ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist     = 5
> ns_type     = grid
> rlist       = 1.4
> rcoulomb    = 1.4
> rvdw        = 1.4
> ; PME electrostatics parameters
> coulombtype     = PME
> fourierspacing  = 0.12
> fourier_nx      = 0
> fourier_ny      = 0
> fourier_nz      = 0
> pme_order       = 4
> ewald_rtol      = 1e-5
> optimize_fft    = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl      = Nose-Hoover
> tc_grps     = Protein   NAD
> tau_t       = 0.5       0.5
> ref_t       = 310       310
> ; Pressure coupling is on
> Pcoupl          = Parrinello-Rahman
> pcoupltype      = isotropic
> tau_p           = 1.0
> compressibility = 4.5e-5
> ref_p           = 1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel     = no
> ; Periodic boundary conditions are on in all directions
> pbc     = xyz
> ; Long-range dispersion correction
> DispCorr    = EnerPres
> ; Pull code
> pull                    = yes
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = NAD
> pull_group2_name        = Protein
> pull_coord1_type        = umbrella      ; harmonic biasing force
> pull_coord1_geometry    = distance      ; simple distance increase
> pull_coord1_groups      = 1 2
> pull_coord1_dim         = N N Y
> pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
> pull_coord1_start       = yes           ; define initial COM distance > 0
>
>
> Please let me know where I'm making the mistake.
>

You're using an outdated version of GROMACS that does not recognize the new 
syntax that was introduced in version 5.1.

-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

==================================================