Wed Dec 28 11:03:23 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 11:03:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 0.5557464 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): -11.93100 28.16100 ymin,ymax (A): 30.09700 78.61500 zmin,zma (A): 8.941000 72.99900 x,y,z range (A): 40.09200 48.51800 64.05800 scale (grids/A): 0.5557464 object centre (A): 8.115000 54.35600 40.97000 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 4.681010 assigned positive charge : 291.1720 centred at (gu) : 90.21220 90.01580 89.97688 assigned negative charge : -286.4913 centred at (gu) : 90.04158 90.01318 89.97994 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4034 nv = 96 ne = 84 npr = 39803 no. pairs analyzed = 39803 no. exposed pairs = 2579 no. arc points = 17940 no. surface atoms = 868 nbur = 1101 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 = 1.568000 m= 154 mr = 2108 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1823 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 5146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4438567E-10 4.0222020E-10 midg,1,midg; midg,igrid,midg 4.0561390E-10 4.4087861E-10 1,midg,midg; igrid,midg,midg -6.1239275E-10 1.5257813E-09 gauss-seidel spectral radius is 0.9832200 estimated iterations to convergence 64 setup time was (sec) 0.7500000 now iterating at: 11:03:25 rms-change max change #iterations 6.3740306E-02 12.06117 at 10iterations 4.6396400E-03 0.8721695 at 20iterations 3.1573192E-04 5.9936523E-02 at 30iterations 2.1779691E-05 4.4577122E-03 at 40iterations 1.5138556E-06 3.0708313E-04 at 50iterations finished qdiffx linear iterations at : 11:03:32 total time elapsed so far: 7.800000 # loops : 50 mean,max change (kT/e) : 1.5138556E-06 3.0708313E-04 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 11:03:33 8.001u 0.678s 0:09.83 88.1% 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 11:03:33 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 1.667239 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): -11.93100 28.16100 ymin,ymax (A): 30.09700 78.61500 zmin,zma (A): 8.941000 72.99900 x,y,z range (A): 40.09200 48.51800 64.05800 scale (grids/A): 1.667239 object centre (A): 8.115000 54.35600 40.97000 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 4.681010 assigned positive charge : 291.1720 centred at (gu) : 90.63657 90.04741 89.93041 assigned negative charge : -286.4913 centred at (gu) : 90.12490 90.03962 89.94015 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 43853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17940 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 13977 mr = 29210 m= 1525 mr = 10124 m= 34 mr = 870 m= 0 mr = 8 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 569 time to turn everything in is 0.4100000 number of dielectric boundary points 19177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14122 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) : 0.5557464 object centre at (A) : 8.115000 54.35600 40.97000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9957392E-02 1.9916343E-02 midg,1,midg; midg,igrid,midg 1.5255278E-04 2.7482898E-04 1,midg,midg; igrid,midg,midg -7.3440317E-03 7.1572559E-03 gauss-seidel spectral radius is 0.9981395 estimated iterations to convergence 184 setup time was (sec) 0.7900000 now iterating at: 11:03:35 rms-change max change #iterations 2.699480 129.4773 at 10iterations 1.107036 49.07990 at 20iterations 0.4580064 19.33538 at 30iterations 0.1894177 8.687224 at 40iterations 7.7519201E-02 3.241073 at 50iterations 3.2093544E-02 1.467661 at 60iterations 1.3257543E-02 0.5182476 at 70iterations 5.4428978E-03 0.2370791 at 80iterations 2.2352727E-03 0.1067421 at 90iterations 9.2097558E-04 4.2041779E-02 at 100iterations 3.8149455E-04 1.7211914E-02 at 110iterations 1.5701501E-04 6.5078735E-03 at 120iterations finished qdiffx linear iterations at : 11:03:51 total time elapsed so far: 17.44000 # loops : 120 mean,max change (kT/e) : 1.5701501E-04 6.5078735E-03 energy calculations done at 17.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.61000 DelPhi exited at 11:03:52 17.613u 0.648s 0:18.66 97.8% 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 11:03:52 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 2.500859 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): -11.93100 28.16100 ymin,ymax (A): 30.09700 78.61500 zmin,zma (A): 8.941000 72.99900 x,y,z range (A): 40.09200 48.51800 64.05800 scale (grids/A): 2.500859 object centre (A): 8.115000 54.35600 40.97000 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 4.681010 assigned positive charge : 291.1720 centred at (gu) : 90.95482 90.07118 89.89564 assigned negative charge : -286.4913 centred at (gu) : 90.18738 90.05948 89.91018 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 101638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17940 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 48090 mr = 71297 m= 14412 mr = 38879 m= 2405 mr = 11579 m= 162 mr = 1646 m= 2 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 2011 time to turn everything in is 1.110000 number of dielectric boundary points 43213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 14686 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) : 1.667239 object centre at (A) : 8.115000 54.35600 40.97000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1859618 0.1883005 midg,1,midg; midg,igrid,midg -1.9403575E-02 -1.7942667E-02 1,midg,midg; igrid,midg,midg -0.1170883 9.1821350E-02 gauss-seidel spectral radius is 0.9990901 estimated iterations to convergence 262 setup time was (sec) 1.730000 now iterating at: 11:03:55 rms-change max change #iterations 6.843926 319.6210 at 10iterations 3.745018 113.1130 at 20iterations 2.039947 78.46311 at 30iterations 1.105736 28.60484 at 40iterations 0.5973300 14.94446 at 50iterations 0.3219753 8.566440 at 60iterations 0.1745354 5.962025 at 70iterations 9.4064578E-02 2.382309 at 80iterations 5.0606288E-02 1.240021 at 90iterations 2.7369801E-02 0.6884909 at 100iterations 1.4770564E-02 0.3442917 at 110iterations 7.9663908E-03 0.2058595 at 120iterations 4.2927745E-03 0.1028366 at 130iterations 2.3152607E-03 5.8707595E-02 at 140iterations 1.2509801E-03 3.1799316E-02 at 150iterations 6.7215151E-04 1.7578125E-02 at 160iterations 3.6321513E-04 9.0484619E-03 at 170iterations 1.9620206E-04 5.5980682E-03 at 180iterations finished qdiffx linear iterations at : 11:04:22 total time elapsed so far: 28.94000 # loops : 180 mean,max change (kT/e) : 1.9620206E-04 5.5980682E-03 energy calculations done at 28.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.11000 DelPhi exited at 11:04:23 29.115u 0.875s 0:30.42 98.5% 0+0k 0+0io 0pf+0w