Wed Dec 21 14:21:58 PST 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 Wed Dec 21 2011 at 14:22:04 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6401151 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): -6.221000 34.90600 ymin,ymax (A): -3.482000 48.52400 zmin,zma (A): -24.46700 31.14800 x,y,z range (A): 41.12700 52.00600 55.61500 scale (grids/A): 0.6401151 object centre (A): 14.34250 22.52100 3.340501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 90.78180 92.59560 90.17951 assigned negative charge : -289.8262 centred at (gu) : 90.89745 92.74508 90.11677 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5602 nv = 96 ne = 84 npr = 39612 no. pairs analyzed = 39612 no. exposed pairs = 2471 no. arc points = 17576 no. surface atoms = 834 nbur = 1130 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3156 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1774 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0105939E-09 9.1095460E-09 midg,1,midg; midg,igrid,midg 9.2742329E-09 -1.7567976E-08 1,midg,midg; igrid,midg,midg 1.1210830E-08 -8.0657436E-09 gauss-seidel spectral radius is 0.9873018 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 14:22:09 rms-change max change #iterations 0.1264923 17.38200 at 10iterations 1.2439721E-02 2.204418 at 20iterations 1.2138354E-03 0.1830215 at 30iterations 1.2360785E-04 1.9790888E-02 at 40iterations 1.1910118E-05 1.7204285E-03 at 50iterations finished qdiffx linear iterations at : 14:22:13 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.1910118E-05 1.7204285E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 14:22:22 3.551u 0.218s 0:20.11 18.6% 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 Wed Dec 21 2011 at 14:22:25 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.920345 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): -6.221000 34.90600 ymin,ymax (A): -3.482000 48.52400 zmin,zma (A): -24.46700 31.14800 x,y,z range (A): 41.12700 52.00600 55.61500 scale (grids/A): 1.920345 object centre (A): 14.34250 22.52100 3.340501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 92.34533 97.78672 90.53827 assigned negative charge : -289.8262 centred at (gu) : 92.69260 98.23542 90.35034 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17576 grid for indexing accessible points = 1.400000 m= 22998 mr = 41327 m= 3902 mr = 17764 m= 210 mr = 2656 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2179 time to turn everything in is 0.3700000 number of dielectric boundary points 25093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 14435 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) : 0.6401151 object centre at (A) : 14.34250 22.52100 3.340501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7691996E-02 9.5608328E-03 midg,1,midg; midg,igrid,midg 3.1179143E-02 -1.7532395E-02 1,midg,midg; igrid,midg,midg 7.6336716E-03 -4.1340557E-03 gauss-seidel spectral radius is 0.9985818 estimated iterations to convergence 210 setup time was (sec) 0.7500000 now iterating at: 14:22:26 rms-change max change #iterations 3.675304 166.4741 at 10iterations 1.698311 59.86534 at 20iterations 0.7866778 28.22565 at 30iterations 0.3643059 12.54577 at 40iterations 0.1670862 5.809123 at 50iterations 7.7178411E-02 2.782410 at 60iterations 3.5413388E-02 1.419899 at 70iterations 1.6411617E-02 0.6081295 at 80iterations 7.5661903E-03 0.2488823 at 90iterations 3.4844680E-03 0.1193585 at 100iterations 1.6083521E-03 5.4108858E-02 at 110iterations 7.4485206E-04 2.3998737E-02 at 120iterations finished qdiffx linear iterations at : 14:22:36 total time elapsed so far: 10.18000 # loops : 120 mean,max change (kT/e) : 7.4485206E-04 2.3998737E-02 energy calculations done at 10.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.31000 DelPhi exited at 14:22:48 10.314u 0.461s 0:23.80 45.2% 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 Wed Dec 21 2011 at 14:22:49 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.880518 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): -6.221000 34.90600 ymin,ymax (A): -3.482000 48.52400 zmin,zma (A): -24.46700 31.14800 x,y,z range (A): 41.12700 52.00600 55.61500 scale (grids/A): 2.880518 object centre (A): 14.34250 22.52100 3.340501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 93.51788 101.6801 90.80750 assigned negative charge : -289.8262 centred at (gu) : 94.03894 102.3531 90.52555 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 138082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17576 grid for indexing accessible points = 1.400000 m= 72882 mr = 99893 m= 28318 mr = 60876 m= 7087 mr = 23627 m= 963 mr = 5629 m= 51 mr = 668 m= 0 mr = 24 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 7308 time to turn everything in is 0.8200000 number of dielectric boundary points 56666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14656 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) : 1.920345 object centre at (A) : 14.34250 22.52100 3.340501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9695985 -1.1275209E-02 midg,1,midg; midg,igrid,midg 0.3367753 -0.1891570 1,midg,midg; igrid,midg,midg 4.7358409E-02 -2.5992224E-02 gauss-seidel spectral radius is 0.9992310 estimated iterations to convergence 285 setup time was (sec) 1.220000 now iterating at: 14:22:50 rms-change max change #iterations 8.682323 351.9056 at 10iterations 4.991207 183.4416 at 20iterations 2.840785 76.39516 at 30iterations 1.619232 40.82526 at 40iterations 0.9246143 20.87515 at 50iterations 0.5253187 11.43783 at 60iterations 0.2987476 6.943701 at 70iterations 0.1696450 3.672157 at 80iterations 9.6403062E-02 1.943225 at 90iterations 5.4741915E-02 1.170581 at 100iterations 3.1005479E-02 0.6773987 at 110iterations 1.7657284E-02 0.3714828 at 120iterations 1.0007100E-02 0.2032599 at 130iterations 5.6692064E-03 0.1128216 at 140iterations 3.2205440E-03 6.6410065E-02 at 150iterations 1.8252921E-03 3.4326553E-02 at 160iterations 1.0382541E-03 2.1257401E-02 at 170iterations 5.8846461E-04 1.1537552E-02 at 180iterations finished qdiffx linear iterations at : 14:23:07 total time elapsed so far: 18.07000 # loops : 180 mean,max change (kT/e) : 5.8846461E-04 1.1537552E-02 energy calculations done at 18.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.20000 DelPhi exited at 14:23:09 18.202u 0.434s 0:20.57 90.5% 0+0k 0+0io 0pf+0w