sai nitin wrote:
Hi all,
I recently started molecular dynamics with gromacs performing
protein-ligand simulations for my project first i worked out example
from justin tutorials on protein ligand system and trying to apply to my
protein and ligand.
First i generated topology for my protein using pdbgmx and then i used
PRODRG tool ligand topology has been generated then i included
ligand.itp file in topol.top file and pasted ligand.gro which is
generated from PRODRG tool in protein.gro as suggested in tutorial but
problem comes now
while running editconf as follows warning bad box
editconf -f protein .gro -o box.gro -bt cubic -d 1.0
*WARNING: Bad box in file protein.gro*
Generated a cubic box 5.553 x 4.382 x 4.434
Read 2053 atoms
Volume: 107.894 nm^3, corresponds to roughly 48500 electrons
No velocities found
system size : 5.553 4.382 4.434 (nm)
diameter : 6.093 (nm)
center : 0.068 -0.079 0.153 (nm)
box vectors : 5.553 4.382 4.434 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 107.89 (nm^3)
shift : 3.978 4.126 3.894 (nm)
new center : 4.047 4.047 4.047 (nm)
new box vectors : 8.093 8.093 8.093 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 530.06 (nm^3)
Actually this problem is already been raised from some one else in
gromacs discussion list i tried to use that solution but it is not
helping me
Can any body tell me where i am going wrong..
Did you remember to increment the number of atoms on the second line of the .gro
file after adding the ligand?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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