[gmx-users] Genion error

chandran karunakaran ckaru2000 at yahoo.com
Fri Mar 4 10:22:51 CET 2005

Hi GMX users,

   I am a begniner of GMX. I started with myoglobin.
The charge of the protein is -2. So I added 2 Na+ ions

using genion. Thereafter, I modified the topology file
by including #include "ions.itp", 2 Na+ ions and
pr.mdp as suggested in protein-drug interaction
When I run  this 
"grompp -f pr.mdp -c myo_b4pr.gro -p temp.top -o
I got the following error message. However, for
protein like upiquitin, there is no problem.

Back Off! I just backed up mdout.mdp to
WARNING 1 [file pr.mdp, line unknown]:
  Unknown left-hand warnings in parameter file

Warning: as of GMX v 2.0 unit of compressibility is
truly 1/bar
checking input for internal consistency...
calling c:/gromacs/bin/cpp...
processing topology...
Excluding 3 bonded neighbours for Protein            
turning all bonds into constraints...
Excluding 1 bonded neighbours for SOL              
turning all bonds into constraints...
Excluding 1 bonded neighbours for SOL             
Excluding 1 bonded neighbours for NA                 
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at
300 K
Reading position restraint coords from myo_b4pr.gro
renumbering atomtypes...
converting bonded parameters...
#     ANGLES:   9492
#      PDIHS:   4275
#      IDIHS:   4140
#       LJ14:   8538
#     POSRES:   2530
#     CONSTR:   4857
#     SETTLE:   9590
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file
There are:  4799      OTHER residues
There are:   153    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 48
Fatal error: Not enough ref_t and tau_t values!

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