------------------------------------------------------- PBSA VERSION 2009 UC Irvine ------------------------------------------------------- | Run on 12/08/2011 at 15:48:12 [-O]verwriting output File Assignments: | MDIN: mdin | MDOUT: at.out |INPCRD: ../pbsa_aug_c2/prmtop-inpcrd/at.inpcrd | PARM: ../pbsa_aug_c2/prmtop-inpcrd/at.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=3,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 = 03/31/05 Time = 15:25:15 NATOM = 36 NTYPES = 9 NBONH = 15 MBONA = 22 NTHETH = 29 MTHETA = 31 NPHIH = 43 MPHIA = 46 NHPARM = 0 NPARM = 0 NNB = 163 NRES = 2 NBONA = 22 NTHETA = 31 NPHIA = 46 NUMBND = 25 NUMANG = 42 NPTRA = 23 NATYP = 18 NPHB = 0 IFBOX = 0 NMXRS = 18 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 1376 | Hollerith 220 | Integer 19378 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 87 kbytes -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- 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: 648 648 no. of atoms processed in PB initialization: 36 NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI 1 DA H2 H5 0.059800 0.000000 0.000000 1.000000 1.000000 2 DA C2 CQ 0.571600 0.631400 -0.872700 1.700000 1.700000 3 DA N1 NC -0.762400 -0.762400 0.558700 1.550000 1.550000 4 DA C6 CA 0.689700 0.689700 -0.079100 1.700000 1.700000 5 DA C5 CB 0.072500 0.072500 0.524700 1.700000 1.700000 6 DA C4 CB 0.380000 0.380000 -0.316000 1.700000 1.700000 7 DA N9 N* -0.026800 -0.026800 0.806899 1.550000 1.550000 8 DA C1' CT 0.043100 0.105299 0.078499 1.700000 1.700000 9 DA H33 H1 0.020733 0.000000 0.000000 1.000000 1.000000 10 DA H34 H1 0.020733 0.000000 0.000000 1.000000 1.000000 11 DA H35 H1 0.020733 0.000000 0.000000 1.000000 1.000000 12 DA C8 CK 0.160700 0.348400 -0.295900 1.700000 1.700000 13 DA H8 H5 0.187700 0.000000 0.000000 1.000000 1.000000 14 DA N7 NB -0.617500 -0.617500 -0.196600 1.550000 1.550000 15 DA N6 N2 -0.912300 -0.078900 0.610800 1.550000 1.550000 16 DA H61 H 0.416700 0.000000 0.000000 1.000000 1.000000 17 DA H62 H 0.416700 0.000000 0.000000 1.000000 1.000000 18 DA N3 NC -0.741700 -0.741700 0.269700 1.550000 1.550000 19 DT H73 HC 0.077000 0.000000 0.000000 1.000000 1.000000 20 DT C7 CT -0.226900 0.004100 0.006600 1.700000 1.700000 21 DT H71 HC 0.077000 0.000000 0.000000 1.000000 1.000000 22 DT H72 HC 0.077000 0.000000 0.000000 1.000000 1.000000 23 DT C5 CM 0.002500 0.002500 0.565800 1.700000 1.700000 24 DT C4 C 0.519400 0.519400 -0.126400 1.700000 1.700000 25 DT O4 O -0.556300 -0.556300 -0.036900 1.500000 1.500000 26 DT N3 NA -0.434000 -0.092000 0.995100 1.550000 1.550000 27 DT H3 H 0.342000 0.000000 0.000000 1.000000 1.000000 28 DT C6 CM -0.220900 0.039800 0.018400 1.700000 1.700000 29 DT H6 H4 0.260700 0.000000 0.000000 1.000000 1.000000 30 DT N1 N* -0.023900 -0.023900 0.710400 1.550000 1.550000 31 DT C1' CT 0.068000 0.126800 0.102900 1.700000 1.700000 32 DT H33 H1 0.019600 0.000000 0.000000 1.000000 1.000000 33 DT H34 H1 0.019600 0.000000 0.000000 1.000000 1.000000 34 DT H35 H1 0.019600 0.000000 0.000000 1.000000 1.000000 35 DT C2 C 0.567700 0.567700 -0.136300 1.700000 1.700000 36 DT O2 O -0.588100 -0.588100 -0.020400 1.500000 1.500000 total system charges (+/-) for PB 0.0000 5.1108 -5.1108 cavity_surften = 0.0436 cavity_offset = -1.0080 SAS Surface: surface dots generated: 366 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- 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 522 ======== Setting up Grid Parameters ======== Using bounding box for grid setup Bounding Box at level: 1 Bounding Box Center: 0.000 0.500 3.500 Xmin, Xmax, Xmax-Xmin: -6.625 6.702 13.327 Ymin, Ymax, Ymax-Ymin: -6.074 7.400 13.474 Zmin, Zmax, Zmax-Zmin: 1.040 5.918 4.878 beginning box center at level 1 0.000 0.500 3.500 Grid dimension at level 1 81 83 31 Grid origin corrected at level 1 -20.500 -20.500 -4.500 ------- VMD goodie -------- #First Level Geometric Box draw materials off draw color green draw line " -20.500 -20.500 -4.500" " 20.000 -20.500 -4.500" draw line " -20.500 -20.500 -4.500" " -20.500 21.000 -4.500" draw line " -20.500 -20.500 -4.500" " -20.500 -20.500 11.000" draw line " 20.000 -20.500 -4.500" " 20.000 21.000 -4.500" draw line " 20.000 -20.500 -4.500" " 20.000 -20.500 11.000" draw line " -20.500 21.000 -4.500" " 20.000 21.000 -4.500" draw line " -20.500 21.000 -4.500" " -20.500 21.000 11.000" draw line " -20.500 -20.500 11.000" " 20.000 -20.500 11.000" draw line " -20.500 -20.500 11.000" " -20.500 21.000 11.000" draw line " 20.000 21.000 11.000" " 20.000 21.000 -4.500" draw line " 20.000 21.000 11.000" " -20.500 21.000 11.000" draw line " 20.000 21.000 11.000" " 20.000 -20.500 11.000" #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 1841 Number of SA arcs generated 330 Number of SA arc points exposed 4923 with resolution (A) = .625000E-01 Atomic solvent accessible surface area: 1 9.6905257983517 2 19.4672308050150 3 5.3783036199079 4 7.9188735478027 5 6.5990612898356 6 7.2589674188192 7 0.8963839366513 8 31.6754941912109 9 13.4480766181208 10 9.0972283004935 11 13.4480766181208 12 23.7566206434082 13 16.2167982747927 14 23.0071877073838 15 18.5252680241272 16 0.0000000000000 17 15.0302032790762 18 18.8240626696777 19 16.6123299400315 20 26.3962451593424 21 16.0190324421733 22 9.2949941331129 23 4.9492959673767 24 9.2386858057698 25 20.7901331541168 26 4.7807143288070 27 0.0000000000000 28 15.1778409666219 29 13.0525449528819 30 1.4939732277522 31 30.6856349977356 32 13.2503107855013 33 7.1195699742992 34 13.4480766181208 35 10.2285449992452 36 29.1639367856361 The gmres dimension is 1432 ======== 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 81 83 31 Grid spacing set to 0.500 Grid boundary -20.500 20.500 -20.500 21.500 -4.500 11.500 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 = -72.0632 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 = 0.4497 EELEC = -54.7071 EPB = -17.8058 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 = -72.0632 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 = 0.4497 EELEC = -54.7071 EPB = -17.8058 RESTRAINT = 0.0000 ECAVITY= 0.0000 EDISPER = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Total time 76.42 | Read prm/crd time 0.00 | Force time 76.42 | Nonbond force 76.42 | PB Nonbond 76.42 | PB FD grid 0.00 | PB Sasa 0.02 | PB FD force 76.39 | PB Set linear sys 0.26 | PB Solver 76.13 | PB SA arc 0.02 | PB SA arc setup 0.00 | PB circle 0.02 | PB exclude 0.00 | PB exmol 0.26 | PB exmol setup 0.01 | PB epsbnd 0.00 | Job began at 15:48:12.244 on 12/08/2011 | Setup done at 15:48:12.248 on 12/08/2011 | Run done at 15:49:28.663 on 12/08/2011 | wallclock() was called 58 times