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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Tue, Dec 10, 2013 at 10:04 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: > Fengxue, > > Something wrong with your water free inpcrd and prmtop files … > > Can you email me directly "off the list" your files to take a look? > Please only process three snapshots so you can email your files over. > > Ray > -- > Ray Luo, Ph.D. > Professor, > Biochemistry, Molecular Biophysics, and > Biomedical Engineering > University of California, Irvine, CA 92697-3900 > > > On Tue, Dec 10, 2013 at 1:49 AM, Fengxue Li <lifx916.126.com> wrote: >> Hi,all >> When I >> >> used the MM-PBSA method as implemented in AMBER 11 to calculate the binding free energy,I >> >> created a solvent box including A and B solvent。this is my file ： mmpbsa.in >> Input file for running PB >> &general >> endframe=50000, verbose=1, >> / >> &pb >> istrng=0.15, fillratio=4, scale=0.5, exdi=19.0 >> / >> MMPBSA -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp comp_mix.prmtop -cp comp.prmtop -rp host.prmtop -lp dea.prmtop -y md1.mdcrd >> to calculate free energy，this error is >> calculating receptor contribution... >> PB Waring in pb_read(): setting grid spacing larger than solvent probe >> may cause numerical instability if ipb=1 >> PB Info in pb_read(): npopt has been overwritten with inp >> Total surface charge 0.0045 >> Reaction field energy -149.3438 >> Cavity solvation energy 11.1404 >> Total surface charge 0.1397 >> Reaction field energy -1523.3429 >> Cavity solvation energy 72.9324 >> Total surface charge 0.1413 >> Reaction field energy -1876.4292 >> Cavity solvation energy 65.1309 >> SA Bomb in circle(): Stored surface points over limit 594240 >> Error: mmpbsa_py_energy error during PB calculations! >> you suggest that i may run with the latest version of AmberTools,Then I >> >> used the MM-PBSA method as implemented in AMBER 12 and AmberTools 13 to calculate the binding free energy,this error is >> >> Beginning PB calculations with /opt/amber12/bin/mmpbsa_py_energy >> calculating complex contribution... >> CalcError: /opt/amber12/bin/mmpbsa_py_energy failed with prmtop comp.prmtop! >> >> >> Exiting. All files have been retained >> >> . >> >> >> >> >> Can anyone help me to calculate freeenergy for this system？ >> Thank you in advance for your help >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Dec 16 2013 - 15:30:02 PST