[gmx-users] about minimizing protein in urea water mixture

[Min Wu]

Hello All,

I just create a urea /water spce co-solvent box (2.8 nm cubic) with amber
forcefield and want to use it to solve my protein. After about 500ps
equilibrium, I solved the protein with the npt.gro (cosolvent). But under
minimization, the force on H11 and H21 of some urea molecules are still
larger than 10 to 4.

Can anyone could give me some suggestions for energy minimization? I
attached my mdp file for energy minimization here.

Thank you so much.

#!/bin/bash

# Molecule name
MOL=2lsb

CDIR=`pwd`
cat >  MinFreezeSol.mdp << _EOF_
include               =  -I$CDIR/ParmFiles -I$CDIR/ParmFiles/MinFreezeSol
define                =  -DPOSRES
;freezegrps            =  STILL MOVE
;freezedim             =  Y Y Y N N N
integrator            =  steep
;constraints           =  all-bonds
constraint_algorithm  =  lincs ; no em with shake
nstxout               =  500
nstlist               =  10
ns_type               =  grid
pbc              =     xyz
coulombtype           =  PME
rvdw                  = 1.5
rlist                 = 1.5
rcoulomb              = 1.5
fourierspacing        = 0.135
pme_order             = 4
ewald_rtol            = 1e-5
;
;       Energy minimizing stuff
;
nsteps              =  500000
emstep              =  0.0001
emtol               =  50.0 ; 100.0
_EOF_

cat >  MinSol.mdp << _EOF_
include               =  -I$CDIR/ParmFiles/MinFreezeSol
define                =  -DPOSRES
integrator            =  steep
constraint_algorithm  =  lincs ; no em with shake
nstxout               =  1000
nstlist               =  10
ns_type               =  grid
pbc               =  xyz
coulombtype           =  PME
rvdw                  = 1.5
rlist                 = 1.5
rcoulomb              = 1.5
fourierspacing        = 0.12
pme_order             = 4
ewald_rtol            = 1e-5
;
;       Energy minimizing stuff
;
nsteps              =  500000
emstep              =  0.0001
emtol               = 50.0; 100.0
_EOF_

cat >  MinSol2.mdp << _EOF_
;include               =  -I$CDIR/ParmFiles -I$CDIR/ParmFiles/MinFreezeSol
;define                =  -DPOSRES
integrator            =  steep
constraint_algorithm  =  lincs ; no em with shake
nstxout               =  1000
nstlist               =  10
ns_type               =  grid
pbc               =  xyz
coulombtype           =  PME
rvdw                  = 1.5
rlist                 = 1.5
rcoulomb              = 1.5
fourierspacing        = 0.12
pme_order             = 4
ewald_rtol            = 1e-5
;
;       Energy minimizing stuff
;
nsteps              =  500000
emstep              =  0.001; 0.0001
emtol               = 40.0; 100.0
_EOF_

# Move restraints files around before minimization"
cp posre_100000.itp posre.itp

echo "1. Minimize SOL - restraints on Prot and DNA heavy atoms and Water O"
CDIR=`pwd`
gmx grompp -f MinFreezeSol.mdp \
        -c ${MOL}_SpcUrNa.gro \
          -p ${MOL}_SpcUrNa.top \
        -o ${MOL}_SpcMin.tpr &> ${MOL}_SpcMin.grompp.out

gmx mdrun -nice 4 \
    -s ${MOL}_SpcMin.tpr \
        -o ${MOL}_SpcMin.trr \
        -e ${MOL}_SpcMin.edr \
        -c ${MOL}_SpcMin.gro -v &> ${MOL}_SpcMin.mdrun.out
echo "Energy minimiz cool restr of Spc finished"

# Move restraints files around before minimization"
/usr/local/gromacs-4.0.7/bin/
cp posre_10000.itp posre.itp

echo "2. Minimize protein with strongest restraint on Protein atoms"
gmx grompp -f MinSol.mdp \
        -c ${MOL}_SpcMin.gro \
          -p ${MOL}_SpcUrNa.top \
        -o ${MOL}_SpcMin2.tpr &> ${MOL}_SpcMin2.grompp.out

gmx mdrun -nice  4\
        -s ${MOL}_SpcMin2.tpr \
        -o ${MOL}_SpcMin2.trr \
        -e ${MOL}_SpcMin2.edr \
        -c ${MOL}_SpcMin2.gro -v &> ${MOL}_SpcMin2.mdrun.out
echo "Energy minimiz strong restraint finished 10000"

# Move restraints files around before minimization"
cp posre_1000.itp posre.itp

echo "3. Minimize protein with very strong restraints on Protein atoms"
gmx grompp -f MinSol.mdp \
        -c ${MOL}_SpcMin2.gro \
          -p ${MOL}_SpcUrNa.top \
        -o ${MOL}_SpcMin3.tpr &> ${MOL}_SpcMin3.grompp.out

##mdrun -nice 4 \
gmx mdrun -nice 4\
        -s ${MOL}_SpcMin3.tpr \
        -o ${MOL}_SpcMin3.trr \
        -e ${MOL}_SpcMin3.edr \
        -c ${MOL}_SpcMin3.gro -v &> ${MOL}_SpcMin3.mdrun.out
echo "Energy minimiz strong restraint Prot finished 1000"

# Move restraints files around before minimization"
cp posre_100.itp posre.itp
echo "4. Minimize protein with strong restraints on Protein atoms"
gmx grompp -f MinSol.mdp \
        -c ${MOL}_SpcMin3.gro \
          -p ${MOL}_SpcUrNa.top \
        -o ${MOL}_SpcMin4.tpr &> ${MOL}_SpcMin4.grompp.out

gmx mdrun -nice 4\
        -s ${MOL}_SpcMin4.tpr \
        -o ${MOL}_SpcMin4.trr \
        -e ${MOL}_SpcMin4.edr \
        -c ${MOL}_SpcMin4.gro -v &> ${MOL}_SpcMin4.mdrun.out
echo "Energy minimiz strong restraint Prot finished 100"

# Move restraints files around before minimization"
cp posre_10.itp posre.itp
echo "5. Minimize protein with weak restraints on Protein atoms"
gmx grompp -f MinSol.mdp \
        -c ${MOL}_SpcMin4.gro \
          -p ${MOL}_SpcUrNa.top \
        -o ${MOL}_SpcMin5.tpr &> ${MOL}_SpcMin5.grompp.out

gmx mdrun -nice 4\
        -s ${MOL}_SpcMin5.tpr \
        -o ${MOL}_SpcMin5.trr \
        -e ${MOL}_SpcMin5.edr \
        -c ${MOL}_SpcMin5.gro -v &> ${MOL}_SpcMin5.mdrun.out
echo "Energy minimiz weak restraint of Prot finished 10"

# Move restraints files around before minimization"
cp posre_0.itp posre.itp
echo "6. Minimize protein with no restraints on Protein atoms 1"
gmx grompp -f MinSol.mdp \
        -c ${MOL}_SpcMin5.gro \
          -p ${MOL}_SpcUrNa.top \
        -o ${MOL}_SpcMin6.tpr &> ${MOL}_SpcMin6.grompp.out

gmx mdrun -nice 4 \
        -s ${MOL}_SpcMin6.tpr \
        -o ${MOL}_SpcMin6.trr \
        -e ${MOL}_SpcMin6.edr \
        -c ${MOL}_SpcMin6.gro -v &> ${MOL}_SpcMin6.mdrun.out
echo "Energy minimiz no restraint of Prot finished - 0:1"
echo "7. Minimize protein with no restraints on Protein atoms 2"
gmx grompp -f MinSol2.mdp \
        -c ${MOL}_SpcMin6.gro \
          -p ${MOL}_SpcUrNa.top \
        -o ${MOL}_SpcMin7.tpr &> ${MOL}_SpcMin7.grompp.out

gmx mdrun -nice 4\
        -s ${MOL}_SpcMin7.tpr \
        -o ${MOL}_SpcMin7.trr \
        -e ${MOL}_SpcMin7.edr \
        -c ${MOL}_SpcMin7.gro -v &> ${MOL}_SpcMin7.mdrun.out
echo "Energy minimiz no restraint on Prot finished  -0:2"