What does the _MMPBSA_complex_pb.mdout file say? It should have a more informative error message.
-Bill
On Aug 3, 2012, at 9:49 AM, zhenquan hu <zhenquanhu.yahoo.com.cn> wrote:
> 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 - 07:30:04 PDT
