Have you got a chance to look at your structures? Any problems?
Also, to make the output more helpful, you can set npbverb=1 after
"fillratio=4,". Let's start from there ...
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
On 8/31/2010 10:32 PM, 宋德寿 wrote:
> Dear all,
>
> I'm doing a free energy run using MMPBSA , but i can not get the FINAL RESULTS of PB caculation
>
>
> Here is the input file:
>
> File generated by MMPBSA.py
> &cntrl
> ntb=0, cut=999.0, nsnb=99999,
> imin=5, maxcyc=0, cutcap=-1, xcap=0,
> ycap=0, zcap=0, idecomp=0, ntpr=1,
> ivcap=0, ntmin=2, igb=10, ipb=1, inp=1,
> /
> &pb
> dbfopt=1, epsin=1, epsout=80, istrng=100.0,
> radiopt=0, sprob=1.4, space=0.5, maxitn=1000, npopt=1
> cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4,
> /
>
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> trajectory generated by ptraj
> minimizing coord set # 1
> PB warning in pb_miccg(): CG l_maxitn exceeded!
> PB warning in pb_miccg(): CG l_maxitn exceeded!
> Total surface charge NaN
> Reaction field energy NaN
> Cavity solvation energy 2.8829
>
>
> Maximum number of minimization cycles reached.
> PB warning in pb_miccg(): CG l_maxitn exceeded!
> PB warning in pb_miccg(): CG l_maxitn exceeded!
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 0.0000E+00 C1 1
>
> BOND = 11.3960 ANGLE = 25.1054 DIHED = 45.2729
> VDWAALS = -1.9922 EEL = 0.0000 EPB = NaN
> 1-4 VDW = 11.3052 1-4 EEL = 0.0000 RESTRAINT = 0.0000
> ECAVITY = 2.8829 EDISPER = 0.0000
> minimization completed, ENE= NaN RMS= NaN
> minimizing coord set # 2
> PB warning in pb_miccg(): CG l_maxitn exceeded!
> PB warning in pb_miccg(): CG l_maxitn exceeded!
> Total surface charge NaN
> Reaction field energy NaN
> Cavity solvation energy 2.8785
>
> Maximum number of minimization cycles reached.
> PB warning in pb_miccg(): CG l_maxitn exceeded!
> PB warning in pb_miccg(): CG l_maxitn exceeded!
>
> FINAL_RESULTS_MMPBSA.dat
>
> Ligand:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -3.6883 2.0508 0.2900
> EEL 0.0000 0.0000 0.0000
>
>
> I hope this helps.
> D.S. Song
>
>
>
> 网易邮箱，没有垃圾邮件的邮箱。
>
>
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Received on Wed Sep 01 2010 - 10:00:04 PDT
