------------------------------------------------------- PBSA VERSION 2009 UC Irvine ------------------------------------------------------- | Run on 09/20/2011 at 10:11:26 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: Cs.out |INPCRD: ../pbsa_aug_c2/prmtop-inpcrd/Cs.inpcrd | PARM: ../pbsa_aug_c2/prmtop-inpcrd/Cs.prmtop | Here is the input file: test of PB reaction field on protein g solvated in a sphere &cntrl ntx=1, imin=1, ipb=5, inp=0 / &pb npbverb=1, epsout=80.0, epsin=1.0, radiopt=0, space=0.5, accept=1e-5, fillratio=4,nfocus = 1, sprob=1.4,dprob=1.4,smoothopt=1 bcopt=6,eneopt=1,solvopt=1,maxitn=1000,sasopt=2 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 12/05/05 Time = 16:50:54 NATOM = 1 NTYPES = 1 NBONH = 0 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 1 NRES = 1 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0 NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0 IFBOX = 0 NMXRS = 1 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 75 | Hollerith 9 | Integer 18013 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 71 kbytes -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- K+ General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, ipb = 5, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 ======== Implicit Solvent Initialization ======== Max Nonbonded Pairs: 1 1 no. of atoms processed in PB initialization: 1 NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI 1 K+ Cs Cs 1.000000 1.000000 1.000000 1.500000 1.500000 total system charges (+/-) for PB 1.0000 1.0000 0.0000 cavity_surften = 0.0436 cavity_offset = -1.0080 SAS Surface: surface dots generated: 366 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- K+ begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NB-update: atom-based nb list 0 ======== Setting up Grid Parameters ======== Using bounding box for grid setup Bounding Box at level: 1 Bounding Box Center: 0.000 0.000 0.000 Xmin, Xmax, Xmax-Xmin: -1.500 1.500 3.000 Ymin, Ymax, Ymax-Ymin: -1.500 1.500 3.000 Zmin, Zmax, Zmax-Zmin: -1.500 1.500 3.000 beginning box center at level 1 0.000 0.000 0.000 Grid dimension at level 1 25 25 25 Grid origin corrected at level 1 -6.500 -6.500 -6.500 ------- VMD goodie -------- #First Level Geometric Box draw materials off draw color green draw line " -6.500 -6.500 -6.500" " 6.000 -6.500 -6.500" draw line " -6.500 -6.500 -6.500" " -6.500 6.000 -6.500" draw line " -6.500 -6.500 -6.500" " -6.500 -6.500 6.000" draw line " 6.000 -6.500 -6.500" " 6.000 6.000 -6.500" draw line " 6.000 -6.500 -6.500" " 6.000 -6.500 6.000" draw line " -6.500 6.000 -6.500" " 6.000 6.000 -6.500" draw line " -6.500 6.000 -6.500" " -6.500 6.000 6.000" draw line " -6.500 -6.500 6.000" " 6.000 -6.500 6.000" draw line " -6.500 -6.500 6.000" " -6.500 6.000 6.000" draw line " 6.000 6.000 6.000" " 6.000 6.000 -6.500" draw line " 6.000 6.000 6.000" " -6.500 6.000 6.000" draw line " 6.000 6.000 6.000" " 6.000 -6.500 6.000" #2nd Level Geometric Box draw color blue draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" draw line " 0.000 0.000 0.000" " 0.000 0.000 0.000" --- End VMD goodie -------- ======== Setting up Solvent Accessibility Data ======== Setting up working radii Number of SA srf points exposed 366 Number of SA arcs generated 0 Number of SA arc points exposed 0 with resolution (A) = .625000E-01 Atomic solvent accessible surface area: 1 105.6831768667606 The gmres dimension is 129 ======== FDPB Summary ======== Do FDPB every 1 steps Nonbonded Update residue cutoff is set to 99.0000000000000 fdpb cutoff is set to 5.0000000000000 sas cutoff is set to 9.0000000000000 nonbonded cutoff is set to 0.0000000000000 Grid Constants Grid dimension 25 25 25 Grid spacing set to 0.500 Grid boundary -6.500 6.500 -6.500 6.500 -6.500 6.500 Dielectric Map Use cavity radii in the prmtop file Use undocumented definition Boundary conditions Physical constants Solute dielectric constant : 1.00000000000000 Solvent dielectric constant : 80.0000000000000 Temperature (K) : 300.000000000000 Ionic strength (mM) : 0.00000000000000 Debye-Huckel parameter (1/A): 0.00000000000000 FD Solver Option Use Modified ICCG solver Iteration data Maximum iterations : 1000 Convergence criteria: 1.000000000000000E-05 Iterations required : 0 Norm of the constant vector: 0.0000000000 Norm of the residual vector: 0.0000000000000 Convergence achieved : NaN NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -90.1744 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000 EELEC = 0.0000 EPB = -90.1744 RESTRAINT = 0.0000 ECAVITY= 0.0000 EDISPER = 0.0000 ------------------------------------------------------------------------------ Maximum number of minimization cycles reached. FINAL RESULTS NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -90.1744 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000 EELEC = 0.0000 EPB = -90.1744 RESTRAINT = 0.0000 ECAVITY= 0.0000 EDISPER = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Total time 3.71 | Read prm/crd time 0.00 | Force time 3.70 | Nonbond force 3.70 | PB Nonbond 3.70 | PB FD grid 0.00 | PB FD force 3.70 | PB Set linear sys 0.00 | PB Solver 3.70 | PB exmol 0.00 | PB exmol setup 0.00 | Job began at 10:11:26.215 on 09/20/2011 | Setup done at 10:11:26.217 on 09/20/2011 | Run done at 10:11:29.921 on 09/20/2011 | wallclock() was called 58 times