Dear Amber Users,
I found a problem on running mmpbsa job in Amber12/AmberTools12
MMPBSA.py -O -i mmpbsa.in -o f.dat -sp com_ions.top -cp com.top -rp rec.top -lp lig.top -y md.trj
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber12/bin/cpptraj
Preparing trajectories for simulation...
4 frames were processed by cpptraj for use in calculation.
Beginning PB calculations with /opt/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /opt/amber12/bin/mmpbsa_py_energy failed with prmtop com.top!
Exiting. All files have been retained.
I checked the program in $AMBERHOME/AmberTools/test by
./test_at_serial.sh and make test.mmpbsa
and all passed
Can anyone give me some suggestions?
Below are my parameters for the MM-PB/SA job
#mmpbsa.in =========================
PB test
&general
startframe=1, endframe=4
/
&pb
istrng=0.150,
/
#===================================
Topology file generated:
# leap.in ===========================
source leaprc.ff12SB
source leaprc.gaff
loadamberparams frcmod.ionsjc_tip3p
loadamberparams lig.frcmod
lig = loadMol2 lig.mol2
rec = loadpdb rec.pdb
com = combine {rec lig}
set default PBRadii mbondi2
saveamberparm com com.top com.crd
saveamberparm rec rec.top rec.crd
saveamberparm lig lig.top lig.crd
solvateoct com TIP3PBOX 10
addions com Na+ 1 Cl- 1
addions com Na+ 1 Cl- 1
...
addions com Na+ 1 Cl- 1
saveamberparm com com_ions.top com_ions.crd
quit
#=====================================
MD simulation with pmemd.MPI
# md.in =============================
Production
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, ntp = 1, taup = 0.2
es_cutoff = 8.0, vdw_cutoff = 9.0,
ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0
ntt = 3, gamma_ln = 2.0, nstlim = 500000, dt = 0.002 ioutfm = 1,
ntpr = 100, ntwx = 1000, ntwr = 1000
ntr=0 ig = -1
#=====================================
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Received on Fri Aug 03 2012 - 07:00:04 PDT
