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
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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