Tue Oct 11 06:39:42 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:39:43 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7096156 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -20.11200 24.68900 ymin,ymax (A): -28.56900 11.07300 zmin,zma (A): -13.50600 36.66200 x,y,z range (A): 44.80100 39.64200 50.16800 scale (grids/A): 0.7096156 object centre (A): 2.288501 -8.748000 11.57800 number of atom coordinates read : 2048 total number of charged atoms : 1918 net assigned charge : 7.025010 assigned positive charge : 310.9191 centred at (gu) : 89.81027 90.54651 89.44534 assigned negative charge : -303.8942 centred at (gu) : 89.62508 90.52486 89.42072 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6966 nv = 96 ne = 84 npr = 41450 no. pairs analyzed = 41450 no. exposed pairs = 2446 no. arc points = 16680 no. surface atoms = 831 nbur = 1217 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 4030 m= 3 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1616 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7724 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5636910E-08 6.7624271E-08 midg,1,midg; midg,igrid,midg 4.6761102E-08 8.1637317E-08 1,midg,midg; igrid,midg,midg -3.4077150E-08 1.4898185E-07 gauss-seidel spectral radius is 0.9896432 estimated iterations to convergence 80 setup time was (sec) 0.4900000 now iterating at: 06:39:43 rms-change max change #iterations 0.1971556 27.59810 at 10iterations 2.5266644E-02 3.578257 at 20iterations 3.3784329E-03 0.4606819 at 30iterations 5.5502588E-04 7.0908189E-02 at 40iterations 1.3155308E-04 1.7948151E-02 at 50iterations finished qdiffx linear iterations at : 06:39:46 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.3155308E-04 1.7948151E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:39:46 3.305u 0.168s 0:03.92 88.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:39:47 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.128847 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -20.11200 24.68900 ymin,ymax (A): -28.56900 11.07300 zmin,zma (A): -13.50600 36.66200 x,y,z range (A): 44.80100 39.64200 50.16800 scale (grids/A): 2.128847 object centre (A): 2.288501 -8.748000 11.57800 number of atom coordinates read : 2048 total number of charged atoms : 1918 net assigned charge : 7.025010 assigned positive charge : 310.9191 centred at (gu) : 89.43064 91.63968 88.33597 assigned negative charge : -303.8942 centred at (gu) : 88.87538 91.57475 88.26241 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16680 grid for indexing accessible points = 1.400000 m= 29516 mr = 52968 m= 5689 mr = 22377 m= 524 mr = 3808 m= 9 mr = 260 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 30432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15244 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7096156 object centre at (A) : 2.288501 -8.748000 11.57800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5788761E-02 4.2403329E-02 midg,1,midg; midg,igrid,midg 4.9963966E-03 3.2609615E-02 1,midg,midg; igrid,midg,midg 1.3772405E-02 4.0040981E-02 gauss-seidel spectral radius is 0.9988323 estimated iterations to convergence 232 setup time was (sec) 0.8200000 now iterating at: 06:39:48 rms-change max change #iterations 4.567353 208.6606 at 10iterations 2.255430 83.12842 at 20iterations 1.122449 37.29884 at 30iterations 0.5576902 17.17844 at 40iterations 0.2772957 8.681303 at 50iterations 0.1379663 4.648361 at 60iterations 6.8579964E-02 2.044403 at 70iterations 3.4300841E-02 1.036230 at 80iterations 1.7181268E-02 0.5447998 at 90iterations 8.6626364E-03 0.2358799 at 100iterations 4.3728696E-03 0.1308426 at 110iterations 2.2642380E-03 6.4582825E-02 at 120iterations finished qdiffx linear iterations at : 06:39:54 total time elapsed so far: 7.150000 # loops : 120 mean,max change (kT/e) : 2.2642380E-03 6.4582825E-02 energy calculations done at 7.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 06:39:54 7.330u 0.229s 0:07.84 96.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:39:54 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2048 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.193270 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -20.11200 24.68900 ymin,ymax (A): -28.56900 11.07300 zmin,zma (A): -13.50600 36.66200 x,y,z range (A): 44.80100 39.64200 50.16800 scale (grids/A): 3.193270 object centre (A): 2.288501 -8.748000 11.57800 number of atom coordinates read : 2048 total number of charged atoms : 1918 net assigned charge : 7.025010 assigned positive charge : 310.9191 centred at (gu) : 89.14606 92.45956 87.50405 assigned negative charge : -303.8942 centred at (gu) : 88.31314 92.36220 87.39364 start vw surface at 0.1400000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 170881 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16680 grid for indexing accessible points = 1.400000 m= 92257 mr = 127437 m= 37236 mr = 76756 m= 10776 mr = 30725 m= 2124 mr = 8336 m= 230 mr = 1516 m= 7 mr = 138 m= 0 mr = 4 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.730000 number of dielectric boundary points 68599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 15344 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.128847 object centre at (A) : 2.288501 -8.748000 11.57800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7161140 0.3435297 midg,1,midg; midg,igrid,midg 2.2499714E-02 0.2525039 1,midg,midg; igrid,midg,midg 0.2630794 0.2983997 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 2.030000 now iterating at: 06:39:57 rms-change max change #iterations 10.16983 402.6562 at 10iterations 6.008665 137.2697 at 20iterations 3.543437 66.93411 at 30iterations 2.086164 39.98153 at 40iterations 1.224990 22.21438 at 50iterations 0.7193774 14.02580 at 60iterations 0.4208966 7.852028 at 70iterations 0.2466287 4.693590 at 80iterations 0.1447330 2.933702 at 90iterations 8.4616214E-02 1.651737 at 100iterations 4.9641121E-02 0.9132519 at 110iterations 2.9219156E-02 0.5097351 at 120iterations 1.7257845E-02 0.3128586 at 130iterations 1.0376678E-02 0.2039032 at 140iterations 6.3893385E-03 0.1204720 at 150iterations 4.0625739E-03 7.2216034E-02 at 160iterations 2.7299710E-03 6.0844421E-02 at 170iterations 1.9393222E-03 3.6746979E-02 at 180iterations finished qdiffx linear iterations at : 06:40:07 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 1.9393222E-03 3.6746979E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 06:40:08 12.495u 0.228s 0:13.15 96.6% 0+0k 0+0io 0pf+0w