Hello Everyone,
I have completed the very nice tutorial for lyzosyme available here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
As I am working with unfolding, I would like to try simulate the
unfolding by adding urea. I have made a urea.gro file (lifting the
coordinates from 3va7.pdb) and wanted to use the gmx insert-molecules
command to insert 300 copies of it. my procedure was the following:
convert pdb file to gro file using gmx pdb2gro, selecting OPLS/AA force
field and the tip4p water model
create a box using: gmx editconf -f lys.gro -o lysBox.gro -c -d 1.0 -bt
cubic
solvate using: gmx solvate -cp lysBox.gro -cs spc216.gro -o lysSolv.gro
-p topol.top
add the urea molecules: grm insert-molecules -f lysSolv.gro -ci
urea.gro -nmol 300 -o lysUrea.gro
this gives me the error message:
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.3078 Coulomb: 0.3078 LJ: 0.3078
System total charge: 0.000
Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Coulomb 0e+00
Grid: 23 x 23 x 23 cells
nri = 33186, nrj = 209128
Try 1143box_margin = 0.2907erlap:
Neighborsearching with a cut-off of 0.3078
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.
NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.
The same is the case if the urea is attempted added to lysBox.gro
instead of lysSolv (so to the box with lyzosyme before I have added
solvent).
Can anyone give me any help with what my problem is? I guess one problem
could be if I ask gromacs to insert urea, where another molecule is
already positioned. Ideally, I would like to replace some water
molecules with urea, but I am not sure how to do that.
my urea.gro is the following - note that it is the copy pasting which
messes up the format. gmx does not complain about it:
Urea
4
UREA C 1 2.340 -9.756 -14.099
UREA O 2 1.153 -9.491 -13.782
UREA N1 3 2.834 -9.467 -15.277
UREA N2 4 3.247 -10.369 -13.324
Any help would be highly appreciated.
Cheers
Martin
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