Mon Oct 10 14:01:07 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+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 Mon Oct 10 2011 at 14:01:08 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3124 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: 0.5439017 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): -39.56400 20.64700 ymin,ymax (A): -0.4859999 51.36100 zmin,zma (A): -0.4730000 64.98000 x,y,z range (A): 60.21100 51.84700 65.45300 scale (grids/A): 0.5439017 object centre (A): -9.458500 25.43750 32.25350 number of atom coordinates read : 3124 total number of charged atoms : 2975 net assigned charge : 0.5000136 assigned positive charge : 463.2189 centred at (gu) : 89.88314 90.94018 90.42754 assigned negative charge : -462.7201 centred at (gu) : 89.94887 90.79625 90.37900 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6037 nv = 96 ne = 84 npr = 62295 no. pairs analyzed = 62295 no. exposed pairs = 4162 no. arc points = 29206 no. surface atoms = 1395 nbur = 1729 mkacc time = 0.1400000 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= 253 mr = 2955 m= 0 mr = 22 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2881 ## 347 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6436908E-10 3.6363174E-10 midg,1,midg; midg,igrid,midg -7.2595358E-10 1.1703981E-09 1,midg,midg; igrid,midg,midg 4.4782511E-10 -3.9432768E-10 gauss-seidel spectral radius is 0.9825888 estimated iterations to convergence 62 setup time was (sec) 0.5900000 now iterating at: 14:01:08 rms-change max change #iterations 7.5666986E-02 12.09801 at 10iterations 5.0876406E-03 0.8789558 at 20iterations 3.5245565E-04 6.3667297E-02 at 30iterations 4.2737280E-05 8.4629059E-03 at 40iterations 1.0736001E-05 2.4192333E-03 at 50iterations finished qdiffx linear iterations at : 14:01:11 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.0736001E-05 2.4192333E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 14:01:12 3.497u 0.206s 0:04.31 85.6% 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 Mon Oct 10 2011 at 14:01:12 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3124 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: 1.631705 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): -39.56400 20.64700 ymin,ymax (A): -0.4859999 51.36100 zmin,zma (A): -0.4730000 64.98000 x,y,z range (A): 60.21100 51.84700 65.45300 scale (grids/A): 1.631705 object centre (A): -9.458500 25.43750 32.25350 number of atom coordinates read : 3124 total number of charged atoms : 2975 net assigned charge : 0.5000136 assigned positive charge : 463.2189 centred at (gu) : 89.64857 92.81970 91.28166 assigned negative charge : -462.7201 centred at (gu) : 89.84624 92.38867 91.13642 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29206 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20730 mr = 43382 m= 2126 mr = 13833 m= 63 mr = 914 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 30785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 280 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 22736 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) : 0.5439017 object centre at (A) : -9.458500 25.43750 32.25350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0497067E-02 -1.0852005E-02 midg,1,midg; midg,igrid,midg -8.8619348E-03 1.5277381E-02 1,midg,midg; igrid,midg,midg -3.8274692E-03 -2.3356574E-03 gauss-seidel spectral radius is 0.9982026 estimated iterations to convergence 187 setup time was (sec) 0.8200000 now iterating at: 14:01:13 rms-change max change #iterations 3.386696 163.7122 at 10iterations 1.409279 58.84338 at 20iterations 0.5881178 20.28275 at 30iterations 0.2461255 8.465469 at 40iterations 0.1029614 3.880399 at 50iterations 4.2971980E-02 1.525692 at 60iterations 1.8018803E-02 0.6714053 at 70iterations 7.5451215E-03 0.2821655 at 80iterations 3.1530270E-03 0.1066818 at 90iterations 1.3204954E-03 5.3590775E-02 at 100iterations 5.5446709E-04 2.0088196E-02 at 110iterations 2.3230190E-04 7.9612732E-03 at 120iterations finished qdiffx linear iterations at : 14:01:20 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.3230190E-04 7.9612732E-03 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 14:01:22 7.777u 0.283s 0:09.76 82.4% 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 Mon Oct 10 2011 at 14:01:22 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3124 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: 2.447558 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): -39.56400 20.64700 ymin,ymax (A): -0.4859999 51.36100 zmin,zma (A): -0.4730000 64.98000 x,y,z range (A): 60.21100 51.84700 65.45300 scale (grids/A): 2.447558 object centre (A): -9.458500 25.43750 32.25350 number of atom coordinates read : 3124 total number of charged atoms : 2975 net assigned charge : 0.5000136 assigned positive charge : 463.2189 centred at (gu) : 89.47260 94.22941 91.92223 assigned negative charge : -462.7201 centred at (gu) : 89.76922 93.58291 91.70452 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 153265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29206 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 70495 mr = 106742 m= 20895 mr = 54694 m= 3252 mr = 15119 m= 245 mr = 1967 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 69551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 23754 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) : 1.631705 object centre at (A) : -9.458500 25.43750 32.25350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4400556 -0.2408509 midg,1,midg; midg,igrid,midg -0.1033385 0.2579024 1,midg,midg; igrid,midg,midg 1.9207217E-02 1.2859509E-02 gauss-seidel spectral radius is 0.9991516 estimated iterations to convergence 271 setup time was (sec) 1.550000 now iterating at: 14:01:24 rms-change max change #iterations 8.993876 311.0016 at 10iterations 5.126935 136.8190 at 20iterations 2.906808 73.75928 at 30iterations 1.635393 37.72187 at 40iterations 0.9158961 22.20514 at 50iterations 0.5124416 11.81992 at 60iterations 0.2847778 6.192363 at 70iterations 0.1583166 3.734791 at 80iterations 8.7843224E-02 1.892845 at 90iterations 4.8738949E-02 0.9485416 at 100iterations 2.6929574E-02 0.5671573 at 110iterations 1.4923524E-02 0.3291397 at 120iterations 8.2530500E-03 0.1864815 at 130iterations 4.5632031E-03 9.2744827E-02 at 140iterations 2.5175512E-03 5.4580688E-02 at 150iterations 1.3901081E-03 3.0029297E-02 at 160iterations 7.6996349E-04 1.5455246E-02 at 170iterations 4.2460929E-04 9.2439651E-03 at 180iterations finished qdiffx linear iterations at : 14:01:35 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 4.2460929E-04 9.2439651E-03 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 14:01:36 12.607u 0.345s 0:14.20 91.1% 0+0k 0+0io 0pf+0w