[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

[Justin Lemkul]

Post by Martin Nors Pedersen
Hello Everyone,
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.
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
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
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.

None of the above is an error. You should be adding the urea before water;
trying to do it afterwards won't work due to lack of available space. There is
no mechanism currently to replace waters with other polyatomic species. See:

http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | [phone]
http://mackerell.umaryland.edu/~jalemkul

==================================================

[Martin Nors Pedersen]

Thank you for the reply Justin!

I'm sorry for being so naive, but I still cannot get it to work.

Trying to follow the procedure described in you link, I got the
following message:
______________________________
GROMACS: gmx genbox, VERSION 5.0.4
Executable: /sware/exp/gromacs/5.0.4/bin/gmx_mpi
Library dir: /sware/exp/gromacs/5.0.4/share/gromacs/top
Command line:
gmx_mpi genbox -f lysBox.gro -o lysUrea.gro -ci urea.gro -nmol 300

This tool has been removed from Gromacs 5.0. Please see
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
for ideas how to perform the same tasks with the new tools.
______________________________

The link in the software message above mentions that "insert-molecules"
should be used instead, but that is the library/package that I could not
get to work yesterday :S

Can anyone help?

Cheers,
Martin

[Justin Lemkul]

Post by Martin Nors Pedersen
Thank you for the reply Justin!
I'm sorry for being so naive, but I still cannot get it to work.
______________________________
GROMACS: gmx genbox, VERSION 5.0.4
Executable: /sware/exp/gromacs/5.0.4/bin/gmx_mpi
Library dir: /sware/exp/gromacs/5.0.4/share/gromacs/top
gmx_mpi genbox -f lysBox.gro -o lysUrea.gro -ci urea.gro -nmol 300
This tool has been removed from Gromacs 5.0. Please see
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
for ideas how to perform the same tasks with the new tools.
______________________________
The link in the software message above mentions that "insert-molecules" should
be used instead, but that is the library/package that I could not get to work
yesterday :S
Can anyone help?

The syntax is identical, just replace "genbox" with "insert-molecules." The
functionality has literally just been split from genbox, which was trying to do
too many things for a simple program. Your command wasn't working before
because you were trying to add urea after water, which won't work.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | [phone]
http://mackerell.umaryland.edu/~jalemkul

==================================================