Sat Oct 15 15:00:59 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+sph.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 Sat Oct 15 2011 at 15:00:59 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 = 2826 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: 0.5543617 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): -23.91600 25.57300 ymin,ymax (A): -23.62200 33.35500 zmin,zma (A): -6.903000 57.31500 x,y,z range (A): 49.48900 56.97700 64.21800 scale (grids/A): 0.5543617 object centre (A): 0.8284998 4.866500 25.20600 number of atom coordinates read : 2826 total number of charged atoms : 2752 net assigned charge : 2.000007 assigned positive charge : 419.3672 centred at (gu) : 91.43541 89.06297 90.92081 assigned negative charge : -417.3685 centred at (gu) : 91.29907 89.15327 90.87583 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5806 nv = 96 ne = 84 npr = 54492 no. pairs analyzed = 54492 no. exposed pairs = 3960 no. arc points = 28237 no. surface atoms = 1314 nbur = 1512 mkacc time = 0.1000000 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 = 1.540000 m= 256 mr = 2729 m= 0 mr = 2 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2912 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7632 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9050563E-10 6.5305655E-10 midg,1,midg; midg,igrid,midg 1.1323491E-09 -4.9921495E-10 1,midg,midg; igrid,midg,midg -7.2261347E-10 1.8252821E-09 gauss-seidel spectral radius is 0.9832210 estimated iterations to convergence 64 setup time was (sec) 0.4100000 now iterating at: 15:01:00 rms-change max change #iterations 7.0904076E-02 12.01536 at 10iterations 5.0542462E-03 0.7648988 at 20iterations 4.0306276E-04 7.7245712E-02 at 30iterations 5.0375216E-05 7.3795319E-03 at 40iterations 9.3827894E-06 1.1234283E-03 at 50iterations finished qdiffx linear iterations at : 15:01:03 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 9.3827894E-06 1.1234283E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 15:01:03 3.538u 0.187s 0:03.99 92.9% 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 Sat Oct 15 2011 at 15:01:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 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: 1.663085 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): -23.91600 25.57300 ymin,ymax (A): -23.62200 33.35500 zmin,zma (A): -6.903000 57.31500 x,y,z range (A): 49.48900 56.97700 64.21800 scale (grids/A): 1.663085 object centre (A): 0.8284998 4.866500 25.20600 number of atom coordinates read : 2826 total number of charged atoms : 2752 net assigned charge : 2.000007 assigned positive charge : 419.3672 centred at (gu) : 94.30539 87.18812 92.76161 assigned negative charge : -417.3685 centred at (gu) : 93.89677 87.45958 92.62725 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28237 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19233 mr = 41343 m= 2010 mr = 12530 m= 51 mr = 953 m= 0 mr = 1 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 30709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 328 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 21193 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) : 0.5543617 object centre at (A) : 0.8284998 4.866500 25.20600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7961885E-03 7.7430187E-03 midg,1,midg; midg,igrid,midg 2.4307780E-03 -9.8464759E-03 1,midg,midg; igrid,midg,midg -7.5630974E-03 2.0572407E-02 gauss-seidel spectral radius is 0.9982550 estimated iterations to convergence 190 setup time was (sec) 0.5400000 now iterating at: 15:01:04 rms-change max change #iterations 3.304905 164.7454 at 10iterations 1.390675 57.48622 at 20iterations 0.5895193 23.68158 at 30iterations 0.2489879 9.283707 at 40iterations 0.1053957 3.590602 at 50iterations 4.4441026E-02 1.537603 at 60iterations 1.8830599E-02 0.7412518 at 70iterations 7.9789022E-03 0.2801685 at 80iterations 3.3950175E-03 0.1370783 at 90iterations 1.4371745E-03 5.1379204E-02 at 100iterations 6.0937228E-04 2.2686005E-02 at 110iterations 2.6099602E-04 1.0465622E-02 at 120iterations finished qdiffx linear iterations at : 15:01:12 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 2.6099602E-04 1.0465622E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 15:01:12 8.038u 0.241s 0:08.86 93.3% 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 Sat Oct 15 2011 at 15:01:12 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 = 2826 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: 2.494627 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): -23.91600 25.57300 ymin,ymax (A): -23.62200 33.35500 zmin,zma (A): -6.903000 57.31500 x,y,z range (A): 49.48900 56.97700 64.21800 scale (grids/A): 2.494627 object centre (A): 0.8284998 4.866500 25.20600 number of atom coordinates read : 2826 total number of charged atoms : 2752 net assigned charge : 2.000007 assigned positive charge : 419.3672 centred at (gu) : 96.45793 85.78191 94.14222 assigned negative charge : -417.3685 centred at (gu) : 95.84486 86.18938 93.94078 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 149491 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28237 grid for indexing accessible points = 1.400000 m= 65518 mr = 102258 m= 19022 mr = 49977 m= 3076 mr = 13812 m= 189 mr = 1922 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 69265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21999 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) : 1.663085 object centre at (A) : 0.8284998 4.866500 25.20600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2983628 0.1908205 midg,1,midg; midg,igrid,midg -1.5271374E-02 -0.1362465 1,midg,midg; igrid,midg,midg -0.1543627 0.2709042 gauss-seidel spectral radius is 0.9991668 estimated iterations to convergence 274 setup time was (sec) 1.050000 now iterating at: 15:01:14 rms-change max change #iterations 8.594481 269.1066 at 10iterations 4.894573 125.1427 at 20iterations 2.778296 75.29453 at 30iterations 1.565661 35.91166 at 40iterations 0.8795625 21.76845 at 50iterations 0.4928080 11.97334 at 60iterations 0.2744467 5.844163 at 70iterations 0.1535191 3.261726 at 80iterations 8.5438937E-02 1.866770 at 90iterations 4.7502644E-02 1.040974 at 100iterations 2.6437027E-02 0.5285611 at 110iterations 1.4693750E-02 0.2991343 at 120iterations 8.1824651E-03 0.1779861 at 130iterations 4.5485375E-03 9.3475342E-02 at 140iterations 2.5335003E-03 5.2257538E-02 at 150iterations 1.4075470E-03 3.0136108E-02 at 160iterations 7.8921078E-04 1.6288757E-02 at 170iterations 4.3925457E-04 8.9092255E-03 at 180iterations finished qdiffx linear iterations at : 15:01:26 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 4.3925457E-04 8.9092255E-03 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 15:01:27 13.174u 0.232s 0:14.49 92.4% 0+0k 0+0io 0pf+0w