[gmx-users] grompp

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Wed May 21 12:05:08 CEST 2014

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

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
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
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

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


"Disturb the Peace of a John Q Citizen" (Urban Dance Squad)

How can I solve this problem? How can I add the path?

best regards

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

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