Wed Feb 15 08:53:58 PST 2012 #!/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+sph_thinner.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 = amb.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 Wed Feb 15 2012 at 08:53:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.8583484 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 0.8583484 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 89.32039 91.68688 90.65911 assigned negative charge : -160.2671 centred at (gu) : 89.34854 91.78932 90.32064 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5724 nv = 96 ne = 84 npr = 25313 no. pairs analyzed = 25313 no. exposed pairs = 1476 no. arc points = 10252 no. surface atoms = 506 nbur = 631 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 523 mr = 3134 m= 4 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.2300000 number of dielectric boundary points 2987 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 590 ## 52 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5120 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0353342E-07 1.9454972E-06 midg,1,midg; midg,igrid,midg 6.2322420E-07 -3.2417766E-08 1,midg,midg; igrid,midg,midg 5.7849422E-07 2.6139693E-07 gauss-seidel spectral radius is 0.9928070 estimated iterations to convergence 95 setup time was (sec) 0.4500000 now iterating at: 08:53:59 rms-change max change #iterations 0.2983831 44.29649 at 10iterations 5.2378114E-02 7.484156 at 20iterations 9.1482829E-03 1.327848 at 30iterations 1.5914264E-03 0.2056208 at 40iterations 2.7589465E-04 3.5258770E-02 at 50iterations finished qdiffx linear iterations at : 08:54:02 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 2.7589465E-04 3.5258770E-02 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 08:54:02 3.239u 0.164s 0:04.19 80.9% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:54:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.575045 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 2.575045 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 87.96153 95.06090 91.97755 assigned negative charge : -160.2671 centred at (gu) : 88.04571 95.36814 90.96205 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 58868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10252 grid for indexing accessible points = 1.400000 m= 25515 mr = 39756 m= 6833 mr = 19666 m= 1052 mr = 4987 m= 91 mr = 653 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1634 time to turn everything in is 0.5200000 number of dielectric boundary points 27244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 8067 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) : 0.8583484 object centre at (A) : -42.45950 40.31850 29.89400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6972373E-02 8.3294630E-02 midg,1,midg; midg,igrid,midg 2.0187503E-02 -1.0424271E-02 1,midg,midg; igrid,midg,midg 1.7332494E-03 1.8466186E-02 gauss-seidel spectral radius is 0.9990628 estimated iterations to convergence 258 setup time was (sec) 0.8000000 now iterating at: 08:54:04 rms-change max change #iterations 4.477221 241.9111 at 10iterations 2.385306 94.91216 at 20iterations 1.268301 41.01722 at 30iterations 0.6766762 23.86788 at 40iterations 0.3600427 11.56057 at 50iterations 0.1924014 6.289504 at 60iterations 0.1022283 3.148058 at 70iterations 5.4405764E-02 1.616289 at 80iterations 2.9008906E-02 0.9034901 at 90iterations 1.5424362E-02 0.4880238 at 100iterations 8.2565639E-03 0.2477603 at 110iterations 4.3823761E-03 0.1283207 at 120iterations finished qdiffx linear iterations at : 08:54:10 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 4.3823761E-03 0.1283207 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 08:54:11 7.383u 0.150s 0:08.19 91.9% 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 Wed Feb 15 2012 at 08:54:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.862568 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 3.862568 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 86.94226 97.59136 92.96640 assigned negative charge : -160.2671 centred at (gu) : 87.06846 98.05222 91.44312 start vw surface at 0.1300000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 134888 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10252 grid for indexing accessible points = 1.400000 m= 74380 mr = 95047 m= 36431 mr = 62128 m= 13701 mr = 30691 m= 3958 mr = 11230 m= 852 mr = 3165 m= 133 mr = 635 m= 6 mr = 107 m= 0 mr = 3 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 5546 time to turn everything in is 1.600000 number of dielectric boundary points 61343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 8072 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) : 2.575045 object centre at (A) : -42.45950 40.31850 29.89400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4317082 0.3954333 midg,1,midg; midg,igrid,midg 3.4434278E-02 -0.1902360 1,midg,midg; igrid,midg,midg -0.1189862 0.1598823 gauss-seidel spectral radius is 0.9993370 estimated iterations to convergence 306 setup time was (sec) 1.900000 now iterating at: 08:54:13 rms-change max change #iterations 9.214607 231.5331 at 10iterations 5.474938 113.9111 at 20iterations 3.252133 62.08793 at 30iterations 1.932214 38.74063 at 40iterations 1.148646 21.48905 at 50iterations 0.6802420 12.51646 at 60iterations 0.4039164 7.188269 at 70iterations 0.2389758 4.345309 at 80iterations 0.1414043 2.332817 at 90iterations 8.3947740E-02 1.428667 at 100iterations 4.9770806E-02 0.9501343 at 110iterations 2.9328676E-02 0.4930401 at 120iterations 1.7402751E-02 0.3542700 at 130iterations 1.0301288E-02 0.1952284 at 140iterations 6.0874950E-03 0.1023365 at 150iterations 3.5997140E-03 5.9051871E-02 at 160iterations 2.1317822E-03 3.8861632E-02 at 170iterations 1.2644416E-03 2.2376537E-02 at 180iterations finished qdiffx linear iterations at : 08:54:23 total time elapsed so far: 11.82000 # loops : 180 mean,max change (kT/e) : 1.2644416E-03 2.2376537E-02 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 08:54:23 12.015u 0.157s 0:12.55 96.8% 0+0k 0+0io 0pf+0w