[gmx-users] Adding urea molecules to lysozyme simulation

[Martin Nors Pedersen]

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