[gmx-users] KALP15-DPPC Tutorial

Justin Lemkul jalemkul at vt.edu
Fri Aug 24 19:41:02 CEST 2012

On 8/24/12 10:48 AM, Shima Arasteh wrote:
> Hi,
> 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?

After the first inflation step and lipids are removed (and the corresponding 
change reflected in the topology), the topology is invariant.  I can offer no 
explanation as to why the first invocation of grompp worked and the subsequent 
one did not, unless you have made other changes or are using the wrong file.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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