[gmx-users] grompp

[Justin Lemkul]

On 5/21/14, 5:34 AM, Urszula Uciechowska wrote:
> Dear Gromacs users,
>
> I am new to Gromacs. I am trying to add ions to my protein system. After
> typing command:
>
> grompp -f grompp.mdp -c EcoLon6mer-sol.gro -p EcoLon6mer.top -o
> genion_input.tpr
>
> where the grompp.mdp contains:
>
> ; ions.mdp - used as input into grompp to generate ions.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 1000.0        ; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps          = 50000         ; Maximum number of (minimization) steps
> to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 1             ; Frequency to update the neighbor list
> and long range forces
> ns_type         = grid          ; Method to determine neighbor list
> (simple, grid)
> rlist           = 1.0           ; Cut-off for making neighbor list (short
> range forces)
> coulombtype     = PME           ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 1.0           ; Short-range electrostatic cut-off
> rvdw            = 1.0           ; Short-range Van der Waals cut-off
> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
>
> I am getting an error message:
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
> checking input for internal consistency...
> processing topology...
> Opening library file
> /software/local/Gromacs/4.5.3/Intel-ompi-fftw/share/gromacs/top/amber99.ff/forcefield.itp
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: futil.c, line: 526
>
> Fatal error:
> Library file ffnonbonded.itp not found in current dir nor in your GMXLIB
> path.
>
> -------------------------------------------------------
>
> "Disturb the Peace of a John Q Citizen" (Urban Dance Squad)
>
> How can I solve this problem? How can I add the path?
>

The force field files should all be in the amber99.ff subdirectory of $GMXLIB. 
Is the file there?  Does it have correct permissions (readable, at least)?

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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