Mon Oct 10 14:01:03 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 Mon Oct 10 2011 at 14:01:03 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: ASL 101 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5677649 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): -20.06800 42.63400 ymin,ymax (A): -23.35200 27.95100 zmin,zma (A): -10.09500 37.48100 x,y,z range (A): 62.70200 51.30300 47.57600 scale (grids/A): 0.5677649 object centre (A): 11.28300 2.299500 13.69300 number of atom coordinates read : 2577 total number of charged atoms : 2435 net assigned charge : 3.900012 assigned positive charge : 387.2217 centred at (gu) : 90.43832 90.11562 90.59430 assigned negative charge : -383.3224 centred at (gu) : 90.27876 90.25037 90.65789 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5554 nv = 96 ne = 84 npr = 49496 no. pairs analyzed = 49496 no. exposed pairs = 3750 no. arc points = 26944 no. surface atoms = 1246 nbur = 1331 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 235 mr = 2547 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2704 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1676262E-09 -2.9511507E-10 midg,1,midg; midg,igrid,midg 2.1555842E-09 -1.2001372E-09 1,midg,midg; igrid,midg,midg -1.3357793E-09 2.7968550E-09 gauss-seidel spectral radius is 0.9839739 estimated iterations to convergence 65 setup time was (sec) 0.8000000 now iterating at: 14:01:05 rms-change max change #iterations 8.2212135E-02 18.04036 at 10iterations 5.9818910E-03 0.9338150 at 20iterations 4.5189861E-04 8.2698822E-02 at 30iterations 3.7962276E-05 6.4898133E-03 at 40iterations 4.8109664E-06 7.2479248E-04 at 50iterations finished qdiffx linear iterations at : 14:01:12 total time elapsed so far: 8.240000 # loops : 50 mean,max change (kT/e) : 4.8109664E-06 7.2479248E-04 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 14:01:13 8.403u 0.738s 0:09.85 92.6% 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 Mon Oct 10 2011 at 14:01:13 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: ASL 101 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.703295 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): -20.06800 42.63400 ymin,ymax (A): -23.35200 27.95100 zmin,zma (A): -10.09500 37.48100 x,y,z range (A): 62.70200 51.30300 47.57600 scale (grids/A): 1.703295 object centre (A): 11.28300 2.299500 13.69300 number of atom coordinates read : 2577 total number of charged atoms : 2435 net assigned charge : 3.900012 assigned positive charge : 387.2217 centred at (gu) : 91.31435 90.34615 91.78229 assigned negative charge : -383.3224 centred at (gu) : 90.83631 90.75083 91.97348 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26944 grid for indexing accessible points = 1.400000 m= 17340 mr = 37835 m= 1851 mr = 11114 m= 55 mr = 784 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 814 time to turn everything in is 0.5700000 number of dielectric boundary points 29971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18849 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) : 0.5677649 object centre at (A) : 11.28300 2.299500 13.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1666399E-02 -2.0562978E-03 midg,1,midg; midg,igrid,midg 1.7277649E-02 -6.3921809E-03 1,midg,midg; igrid,midg,midg -4.2646892E-02 4.3099285E-03 gauss-seidel spectral radius is 0.9983113 estimated iterations to convergence 193 setup time was (sec) 1.110000 now iterating at: 14:01:15 rms-change max change #iterations 3.335184 176.7589 at 10iterations 1.417170 54.86093 at 20iterations 0.6038198 23.31923 at 30iterations 0.2598539 10.14548 at 40iterations 0.1106280 4.873962 at 50iterations 4.7595907E-02 1.757536 at 60iterations 2.0518260E-02 0.7201786 at 70iterations 8.7815905E-03 0.3135509 at 80iterations 3.7593322E-03 0.1369600 at 90iterations 1.6181443E-03 6.8984509E-02 at 100iterations 6.9387921E-04 2.4518490E-02 at 110iterations 2.9920359E-04 1.2109756E-02 at 120iterations finished qdiffx linear iterations at : 14:01:30 total time elapsed so far: 16.05000 # loops : 120 mean,max change (kT/e) : 2.9920359E-04 1.2109756E-02 energy calculations done at 16.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.24000 DelPhi exited at 14:01:31 16.241u 0.851s 0:18.04 94.7% 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 Mon Oct 10 2011 at 14:01:31 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: ASL 101 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.554942 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): -20.06800 42.63400 ymin,ymax (A): -23.35200 27.95100 zmin,zma (A): -10.09500 37.48100 x,y,z range (A): 62.70200 51.30300 47.57600 scale (grids/A): 2.554942 object centre (A): 11.28300 2.299500 13.69300 number of atom coordinates read : 2577 total number of charged atoms : 2435 net assigned charge : 3.900012 assigned positive charge : 387.2217 centred at (gu) : 91.97138 90.51906 92.67334 assigned negative charge : -383.3224 centred at (gu) : 91.25440 91.12608 92.96018 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 140362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26944 grid for indexing accessible points = 1.400000 m= 60103 mr = 93688 m= 16579 mr = 45177 m= 2714 mr = 11679 m= 248 mr = 1673 m= 4 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 2762 time to turn everything in is 1.330000 number of dielectric boundary points 67687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 19470 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) : 1.703295 object centre at (A) : 11.28300 2.299500 13.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1534801 -2.6319221E-02 midg,1,midg; midg,igrid,midg 0.2389375 -6.8663195E-02 1,midg,midg; igrid,midg,midg -0.6647141 -0.2629984 gauss-seidel spectral radius is 0.9991758 estimated iterations to convergence 275 setup time was (sec) 1.900000 now iterating at: 14:01:34 rms-change max change #iterations 8.638512 345.5034 at 10iterations 4.970296 185.2921 at 20iterations 2.835124 75.06386 at 30iterations 1.607666 36.77127 at 40iterations 0.9080266 21.00928 at 50iterations 0.5092210 12.37280 at 60iterations 0.2850720 6.314129 at 70iterations 0.1593588 3.826870 at 80iterations 8.9340582E-02 1.952486 at 90iterations 4.9824093E-02 1.174835 at 100iterations 2.7771454E-02 0.6258698 at 110iterations 1.5466255E-02 0.3512650 at 120iterations 8.6147916E-03 0.1925278 at 130iterations 4.8151561E-03 0.1078176 at 140iterations 2.6809839E-03 5.9650421E-02 at 150iterations 1.4939915E-03 3.3132553E-02 at 160iterations 8.3232130E-04 1.8203259E-02 at 170iterations 4.6276100E-04 1.0542631E-02 at 180iterations finished qdiffx linear iterations at : 14:02:01 total time elapsed so far: 28.99000 # loops : 180 mean,max change (kT/e) : 4.6276100E-04 1.0542631E-02 energy calculations done at 28.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.17000 DelPhi exited at 14:02:02 29.172u 0.726s 0:30.56 97.8% 0+0k 0+0io 0pf+0w