Mon Oct 10 13:58:46 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 Mon Oct 10 2011 at 13:58:47 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 = 3382 !!! WARNING: LLP 1 has a net charge of 1.1100 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: 0.5755488 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): -11.03000 50.82400 ymin,ymax (A): -12.76800 42.35400 zmin,zma (A): 19.54500 75.67800 x,y,z range (A): 61.85400 55.12200 56.13300 scale (grids/A): 0.5755488 object centre (A): 19.89700 14.79300 47.61150 number of atom coordinates read : 3382 total number of charged atoms : 3225 net assigned charge : 4.610018 assigned positive charge : 523.1458 centred at (gu) : 90.81905 89.94221 87.73286 assigned negative charge : -518.5370 centred at (gu) : 90.73439 90.01334 87.72835 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7545 nv = 96 ne = 84 npr = 65437 no. pairs analyzed = 65437 no. exposed pairs = 4531 no. arc points = 32378 no. surface atoms = 1518 nbur = 1864 mkacc time = 0.1900000 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 = 1.484000 m= 403 mr = 3805 m= 2 mr = 33 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 0.4100000 number of dielectric boundary points 4112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3113 ## 302 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2494453E-09 5.6318977E-10 midg,1,midg; midg,igrid,midg 2.4250448E-09 -7.2476314E-10 1,midg,midg; igrid,midg,midg -8.4703372E-10 3.2602627E-09 gauss-seidel spectral radius is 0.9844606 estimated iterations to convergence 66 setup time was (sec) 0.6800000 now iterating at: 13:58:47 rms-change max change #iterations 9.8111734E-02 17.04694 at 10iterations 7.5347018E-03 1.179155 at 20iterations 5.9773080E-04 8.6894989E-02 at 30iterations 7.7761964E-05 1.3286591E-02 at 40iterations 3.4408858E-05 4.8465729E-03 at 50iterations finished qdiffx linear iterations at : 13:58:51 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 3.4408858E-05 4.8465729E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 13:58:52 4.297u 0.295s 0:05.19 88.2% 0+0k 0+0io 6pf+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 13:58:52 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 !!! WARNING: LLP 1 has a net charge of 1.1100 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: 1.726647 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): -11.03000 50.82400 ymin,ymax (A): -12.76800 42.35400 zmin,zma (A): 19.54500 75.67800 x,y,z range (A): 61.85400 55.12200 56.13300 scale (grids/A): 1.726647 object centre (A): 19.89700 14.79300 47.61150 number of atom coordinates read : 3382 total number of charged atoms : 3225 net assigned charge : 4.610018 assigned positive charge : 523.1458 centred at (gu) : 92.45660 89.82561 83.19775 assigned negative charge : -518.5370 centred at (gu) : 92.20307 90.03955 83.18472 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32378 grid for indexing accessible points = 1.400000 m= 27607 mr = 55035 m= 3743 mr = 18725 m= 167 mr = 1936 m= 0 mr = 31 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 38079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24985 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) : 0.5755488 object centre at (A) : 19.89700 14.79300 47.61150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2873346E-02 5.9380569E-03 midg,1,midg; midg,igrid,midg 2.5055848E-02 -5.8187824E-03 1,midg,midg; igrid,midg,midg -9.0074670E-03 -8.1145093E-03 gauss-seidel spectral radius is 0.9984299 estimated iterations to convergence 200 setup time was (sec) 1.060000 now iterating at: 13:58:53 rms-change max change #iterations 4.153955 194.3488 at 10iterations 1.839322 69.76256 at 20iterations 0.8186665 28.50090 at 30iterations 0.3630087 12.46366 at 40iterations 0.1616981 6.096647 at 50iterations 7.1903870E-02 2.376348 at 60iterations 3.1956486E-02 0.9884758 at 70iterations 1.4237606E-02 0.4639578 at 80iterations 6.3431226E-03 0.2185669 at 90iterations 2.8501684E-03 9.8937035E-02 at 100iterations 1.2918115E-03 4.2900085E-02 at 110iterations 6.1704870E-04 2.1583557E-02 at 120iterations finished qdiffx linear iterations at : 13:59:02 total time elapsed so far: 9.880000 # loops : 120 mean,max change (kT/e) : 6.1704870E-04 2.1583557E-02 energy calculations done at 9.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.06000 DelPhi exited at 13:59:03 10.067u 0.343s 0:11.13 93.4% 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 13:59:03 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 !!! WARNING: LLP 1 has a net charge of 1.1100 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: 2.589970 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): -11.03000 50.82400 ymin,ymax (A): -12.76800 42.35400 zmin,zma (A): 19.54500 75.67800 x,y,z range (A): 61.85400 55.12200 56.13300 scale (grids/A): 2.589970 object centre (A): 19.89700 14.79300 47.61150 number of atom coordinates read : 3382 total number of charged atoms : 3225 net assigned charge : 4.610018 assigned positive charge : 523.1458 centred at (gu) : 93.68463 89.73835 79.79629 assigned negative charge : -518.5370 centred at (gu) : 93.30441 90.05931 79.77702 start vw surface at 0.1900000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 190842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32378 grid for indexing accessible points = 1.400000 m= 91562 mr = 134971 m= 29735 mr = 71469 m= 6135 mr = 22202 m= 658 mr = 4023 m= 28 mr = 374 m= 0 mr = 7 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 85914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 25783 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) : 1.726647 object centre at (A) : 19.89700 14.79300 47.61150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2221513 7.4851893E-02 midg,1,midg; midg,igrid,midg 0.3780959 -8.8674925E-02 1,midg,midg; igrid,midg,midg 8.7960325E-02 -0.5689444 gauss-seidel spectral radius is 0.9992278 estimated iterations to convergence 284 setup time was (sec) 2.230000 now iterating at: 13:59:06 rms-change max change #iterations 10.57967 301.9767 at 10iterations 6.275717 170.4029 at 20iterations 3.664621 85.89301 at 30iterations 2.133475 47.60355 at 40iterations 1.231357 26.08314 at 50iterations 0.7084755 15.68828 at 60iterations 0.4077476 8.845291 at 70iterations 0.2330864 5.582868 at 80iterations 0.1335362 2.697271 at 90iterations 7.6404192E-02 1.596832 at 100iterations 4.3606970E-02 0.9716454 at 110iterations 2.4915935E-02 0.5222492 at 120iterations 1.4210401E-02 0.2737360 at 130iterations 8.1101665E-03 0.1498318 at 140iterations 4.6472140E-03 9.9853516E-02 at 150iterations 2.6729149E-03 5.3466797E-02 at 160iterations 1.5698993E-03 3.4466267E-02 at 170iterations 9.5147447E-04 1.9848824E-02 at 180iterations finished qdiffx linear iterations at : 13:59:20 total time elapsed so far: 16.99000 # loops : 180 mean,max change (kT/e) : 9.5147447E-04 1.9848824E-02 energy calculations done at 16.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.19000 DelPhi exited at 13:59:22 17.188u 0.339s 0:18.54 94.4% 0+0k 0+0io 0pf+0w