Wed Dec 28 11:03:29 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 28 2011 at 11:03:29 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.6361573 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): -5.328000 34.92600 ymin,ymax (A): -3.779000 48.63900 zmin,zma (A): -24.24800 31.71300 x,y,z range (A): 40.25400 52.41800 55.96100 scale (grids/A): 0.6361573 object centre (A): 14.79900 22.43000 3.732500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.9999 centred at (gu) : 90.62299 92.50838 89.96888 assigned negative charge : -291.0002 centred at (gu) : 90.75536 92.66640 89.89867 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5464 nv = 96 ne = 84 npr = 40262 no. pairs analyzed = 40262 no. exposed pairs = 2458 no. arc points = 17271 no. surface atoms = 841 nbur = 1129 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 283 mr = 3042 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3400000 number of dielectric boundary points 2666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1788 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6448 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5098730E-09 8.4094056E-09 midg,1,midg; midg,igrid,midg 8.8581791E-09 -1.6799348E-08 1,midg,midg; igrid,midg,midg 1.1546651E-08 -8.5715319E-09 gauss-seidel spectral radius is 0.9871439 estimated iterations to convergence 72 setup time was (sec) 0.6400000 now iterating at: 11:03:30 rms-change max change #iterations 0.1239131 22.70133 at 10iterations 1.2142730E-02 1.892620 at 20iterations 1.1697591E-03 0.1920860 at 30iterations 1.1436047E-04 1.6599655E-02 at 40iterations 1.1029209E-05 1.9731522E-03 at 50iterations finished qdiffx linear iterations at : 11:03:33 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 1.1029209E-05 1.9731522E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 11:03:34 4.396u 0.238s 0:05.39 85.7% 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 Wed Dec 28 2011 at 11:03:34 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.908472 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): -5.328000 34.92600 ymin,ymax (A): -3.779000 48.63900 zmin,zma (A): -24.24800 31.71300 x,y,z range (A): 40.25400 52.41800 55.96100 scale (grids/A): 1.908472 object centre (A): 14.79900 22.43000 3.732500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.9999 centred at (gu) : 91.86845 97.52488 89.90655 assigned negative charge : -291.0002 centred at (gu) : 92.26624 97.99931 89.69619 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 58950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17271 grid for indexing accessible points = 1.400000 m= 21479 mr = 40771 m= 3104 mr = 16377 m= 153 mr = 1976 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1712 time to turn everything in is 0.5900000 number of dielectric boundary points 24511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14464 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) : 0.6361573 object centre at (A) : 14.79900 22.43000 3.732500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9624985E-02 1.4107263E-02 midg,1,midg; midg,igrid,midg 3.2607671E-02 -1.5945788E-02 1,midg,midg; igrid,midg,midg 8.0312332E-03 -7.7719186E-03 gauss-seidel spectral radius is 0.9985621 estimated iterations to convergence 209 setup time was (sec) 0.9100000 now iterating at: 11:03:35 rms-change max change #iterations 3.634971 181.9534 at 10iterations 1.668975 61.27589 at 20iterations 0.7677920 28.72282 at 30iterations 0.3518526 12.86630 at 40iterations 0.1612925 6.276833 at 50iterations 7.3917165E-02 3.081650 at 60iterations 3.3965833E-02 1.264615 at 70iterations 1.5607764E-02 0.5101595 at 80iterations 7.1629398E-03 0.2944622 at 90iterations 3.2887692E-03 0.1175690 at 100iterations 1.5056253E-03 5.4452896E-02 at 110iterations 6.9149793E-04 2.5810242E-02 at 120iterations finished qdiffx linear iterations at : 11:03:43 total time elapsed so far: 8.710000 # loops : 120 mean,max change (kT/e) : 6.9149793E-04 2.5810242E-02 energy calculations done at 8.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.940000 DelPhi exited at 11:03:44 8.946u 0.206s 0:09.85 92.7% 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 Wed Dec 28 2011 at 11:03:44 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.862708 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): -5.328000 34.92600 ymin,ymax (A): -3.779000 48.63900 zmin,zma (A): -24.24800 31.71300 x,y,z range (A): 40.25400 52.41800 55.96100 scale (grids/A): 2.862708 object centre (A): 14.79900 22.43000 3.732500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.9999 centred at (gu) : 92.80284 101.2873 89.85989 assigned negative charge : -291.0002 centred at (gu) : 93.39951 101.9991 89.54430 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 135757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17271 grid for indexing accessible points = 1.400000 m= 69691 mr = 98285 m= 24983 mr = 57993 m= 5467 mr = 20578 m= 656 mr = 4128 m= 32 mr = 456 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 5524 time to turn everything in is 1.450000 number of dielectric boundary points 55138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 14704 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) : 1.908472 object centre at (A) : 14.79900 22.43000 3.732500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9995360 1.3226072E-02 midg,1,midg; midg,igrid,midg 0.3534788 -0.1805106 1,midg,midg; igrid,midg,midg 5.1255371E-02 -5.3904783E-02 gauss-seidel spectral radius is 0.9992242 estimated iterations to convergence 283 setup time was (sec) 1.810000 now iterating at: 11:03:46 rms-change max change #iterations 8.581897 533.4116 at 10iterations 4.909819 116.9986 at 20iterations 2.789251 61.20869 at 30iterations 1.586185 43.61288 at 40iterations 0.8986785 20.21999 at 50iterations 0.5097901 11.17218 at 60iterations 0.2885716 6.016675 at 70iterations 0.1640482 3.420338 at 80iterations 9.2702478E-02 1.949612 at 90iterations 5.2418735E-02 1.067872 at 100iterations 2.9689552E-02 0.5789719 at 110iterations 1.6839936E-02 0.3645711 at 120iterations 9.5504699E-03 0.2052689 at 130iterations 5.4070195E-03 0.1129122 at 140iterations 3.0597029E-03 6.0257435E-02 at 150iterations 1.7288892E-03 3.2211304E-02 at 160iterations 9.7992341E-04 2.0359039E-02 at 170iterations 5.5449159E-04 1.1030912E-02 at 180iterations finished qdiffx linear iterations at : 11:03:59 total time elapsed so far: 14.72000 # loops : 180 mean,max change (kT/e) : 5.5449159E-04 1.1030912E-02 energy calculations done at 14.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.95000 DelPhi exited at 11:04:00 14.955u 0.304s 0:16.23 93.9% 0+0k 0+0io 0pf+0w