[gmx-users] KALP15-DPPC Tutorial

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Aug 24 16:48:35 CEST 2012


I am doing the simulation of kalp15 in DPPC following the Justin's tutorial. 
In the " 2. Pack the lipids around the protein "step, to get the correct area per lipid, I enter these commands:

    #perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
Updating the .top file and adding DPPC 126 to it.

 First minimization:
     Energy minimization with restrained protein
     #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
     #mdrun -deffnm em
     scale down the lipids by a factor of 0.95
     #perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
  Second minimization:
     #grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em_shrink1.tpr  

Then, I get this error:

Fatal error:
number of coordinates in coordinate file (system_shrink1.gro, 6400)
             does not match topology (topol.top, 6438)

Is this not the correct command to start the second minimization? 

Please help me.
Your suggestions are welcomed.


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