I have been unsuccessful at setting up constant pH calculations with my
protein. I am using Amber 11. I would greatly appreciate assistance with
the following:
1) Review the steps below and let me know if my setup is OK (not sure
whether all steps are necessary),
2) I am currently encountering the following error when attempting to
perform STEP 5:
At line 1359 of file _mdread.f (unit = 18, file = 'cpin_1')
Fortran runtime error: Cannot match namelist object name 'residue:
The cpin_1 file is attached. I am hoping to resolve these issues so that I
can live to see another sunrise.
Thanks !!
John K.
STEP 1. Creating prmtop & inpcrd files:
source leaprc.constph
set default PBradii mbondi2
protein1 = loadpdb "protein.pdb"
saveamberparm protein1 prmtop inpcrd
STEP 2. First minimization (protein restrained):
mpirun -np 10 $AMBERHOME/exe/sander.MPI -O -i min_1.in -o min_1.out -c
inpcrd -p prmtop -r min_1.rst < /dev/null &
where, min_1.in:
&cntrl
imin=1, maxcyc=1000, ncyc=500,
ntb=0, igb=2,
cut=30
/
500.0
RES 1 1272
END
END
STEP 3. Second minimization (entire system unrestrained):
mpirun -np 10 $AMBERHOME/exe/sander.MPI -O -i min_2.in -o min_2.out -c
min_1.rst -p prmtop -r min_2.rst < /dev/null &
where, min_2:
&cntrl
imin=1, maxcyc=2500, ncyc=1000,
ntb=0, igb=2,
cut=30
/
STEP 4. Create cpin file:
ambpdb -p prmtop < min_2.rst | cpinutil.pl > cpin_1
STEP 5. Heating over 20 ps (protein restrained):
mpirun -np 10 $AMBERHOME/exe/sander.MPI -O -i md_1.in -o md_1.out -c
min_2.rst -p prmtop -r md1.rst -cpin cpin_1 -cpout cpout_1 -cprestrt
cprestrt_1 < /dev/null &
where, md_1:
&cntrl
imin=0, irest=0, ntx=1,
ntb=0, ntc=2, ntf=2,
cut=30.0,
ntr=1,
nrespa=1,
ig=-1,
ntt=3, gamma_ln=1.0, tempi=0.0, temp0=300.0,
igb=2,
saltcon=0.1,
tol=0.000001,
icnstph=1, solvph=3, ntcnstph=5,
nstlim=10000, dt=0.002,
ntpr=500, ntwx=500, ntwr=1000
/
10.0
RES 1 1272
END
END
STEP 6. Remove excess zero data from cpin_1:
cpinutil.pl cprestrt_1 > cpin_2
STEP 7. Equilibration 100 ps (entire sysyem unrestrained):
mpirun -np 10 $AMBERHOME/exe/sander.MPI -O -i md_2.in -o md_2.out -c
md_1.rst -p prmtop -r md_2.rst -cpin cpin_2 -cpout cpout_2 -cprestrt
cprestrt_2 < /dev/null &
where, md_2:
&cntrl
imin=0, irest=1, ntx=5,
ntb=2, ntc=2, ntf=2,
cut=30.0,
ntr=0,
nrespa=1,
ig=-1,
pres0=1.0,
ntp=1, taup=2,
ntt=3, gamma_ln=1.0, tempi=300.0, temp0=300.0,
igb=2,
saltcon=0.1,
tol=0.000001,
icnstph=1, solvph=3, ntcnstph=5,
nstlim=50000, dt=0.002,
ntpr=500, ntwx=500, ntwr=1000
/
STEP 8. Remove excess zero data from cpin_2:
cpinutil.pl cprestrt_2 > cpin_3
STEP 9. MD production run (10 ns):
mpirun -np 10 $AMBERHOME/exe/sander.MPI -O -i md_3.in -o md_3.out -c
md_2.rst -p prmtop -r md_3.rst -cpin cpin -cpout cpout_3 -cprestrt
cprestrt_3 < /dev/null &
where, md_3:
&cntrl
imin=0, irest=1, ntx=5,
ntb=2, ntc=2, ntf=2,
cut=30.0,
ntr=0,
nrespa=1,
ig=-1,
pres0=1.0,
ntp=1, taup=2,
ntt=3, gamma_ln=1.0, tempi=300.0, temp0=300.0,
igb=2,
saltcon=0.1,
tol=0.000001,
icnstph=1, solvph=3, ntcnstph=5,
nstlim=5000000, dt=0.002,
ntpr=500, ntwx=500, ntwr=1000
/
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Received on Sat Apr 23 2011 - 15:30:03 PDT
