Mon Oct 10 09:25:24 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 09:25:24 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 0.6095577 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): -9.146000 49.25700 ymin,ymax (A): 8.769000 48.01300 zmin,zma (A): -3.752000 38.62900 x,y,z range (A): 58.40300 39.24400 42.38100 scale (grids/A): 0.6095577 object centre (A): 20.05550 28.39100 17.43850 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000011 assigned positive charge : 291.8040 centred at (gu) : 90.08218 89.66544 90.49883 assigned negative charge : -286.8043 centred at (gu) : 90.06751 89.57422 90.59410 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4889 nv = 96 ne = 84 npr = 40078 no. pairs analyzed = 40078 no. exposed pairs = 2468 no. arc points = 17463 no. surface atoms = 838 nbur = 1130 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 233 mr = 2668 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1812 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6000 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6822116E-09 -6.1511068E-10 midg,1,midg; midg,igrid,midg -4.2496306E-10 5.7599476E-09 1,midg,midg; igrid,midg,midg 2.3730642E-09 3.5366492E-09 gauss-seidel spectral radius is 0.9860139 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 09:25:25 rms-change max change #iterations 0.1039257 19.45044 at 10iterations 9.0033310E-03 1.522024 at 20iterations 7.7833724E-04 0.1452484 at 30iterations 6.9421381E-05 1.2786865E-02 at 40iterations 6.1173077E-06 1.0375977E-03 at 50iterations finished qdiffx linear iterations at : 09:25:29 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 6.1173077E-06 1.0375977E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 09:25:29 4.661u 0.379s 0:05.39 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 Mon Oct 10 2011 at 09:25:29 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 1.828673 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): -9.146000 49.25700 ymin,ymax (A): 8.769000 48.01300 zmin,zma (A): -3.752000 38.62900 x,y,z range (A): 58.40300 39.24400 42.38100 scale (grids/A): 1.828673 object centre (A): 20.05550 28.39100 17.43850 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000011 assigned positive charge : 291.8040 centred at (gu) : 90.24664 88.99634 91.49656 assigned negative charge : -286.8043 centred at (gu) : 90.20278 88.72273 91.78235 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 53478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17463 grid for indexing accessible points = 1.400000 m= 18060 mr = 36425 m= 2250 mr = 13488 m= 62 mr = 1338 m= 0 mr = 13 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2478 time to turn everything in is 0.4200000 number of dielectric boundary points 22586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14411 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) : 0.6095577 object centre at (A) : 20.05550 28.39100 17.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8645529E-03 -7.1309938E-04 midg,1,midg; midg,igrid,midg 1.4510390E-03 7.1476907E-03 1,midg,midg; igrid,midg,midg 3.6488064E-02 3.0380303E-02 gauss-seidel spectral radius is 0.9984469 estimated iterations to convergence 201 setup time was (sec) 0.7500000 now iterating at: 09:25:30 rms-change max change #iterations 3.327186 157.3722 at 10iterations 1.475589 61.02968 at 20iterations 0.6589568 26.06543 at 30iterations 0.2917343 11.72582 at 40iterations 0.1306152 4.473186 at 50iterations 5.8038685E-02 2.344048 at 60iterations 2.5849611E-02 0.9489350 at 70iterations 1.1466523E-02 0.4559937 at 80iterations 5.1151556E-03 0.1904297 at 90iterations 2.2799997E-03 9.7071648E-02 at 100iterations 1.0071754E-03 3.8805008E-02 at 110iterations 4.5320860E-04 1.7635822E-02 at 120iterations finished qdiffx linear iterations at : 09:25:40 total time elapsed so far: 10.32000 # loops : 120 mean,max change (kT/e) : 4.5320860E-04 1.7635822E-02 energy calculations done at 10.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.48000 DelPhi exited at 09:25:40 10.485u 0.442s 0:11.23 97.2% 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 09:25:40 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 2.743010 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): -9.146000 49.25700 ymin,ymax (A): 8.769000 48.01300 zmin,zma (A): -3.752000 38.62900 x,y,z range (A): 58.40300 39.24400 42.38100 scale (grids/A): 2.743010 object centre (A): 20.05550 28.39100 17.43850 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000011 assigned positive charge : 291.8040 centred at (gu) : 90.36990 88.49458 92.24485 assigned negative charge : -286.8043 centred at (gu) : 90.30410 88.08405 92.67359 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 123454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17463 grid for indexing accessible points = 1.400000 m= 60191 mr = 88047 m= 19942 mr = 49463 m= 3810 mr = 16199 m= 308 mr = 2875 m= 11 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 8302 time to turn everything in is 1.100000 number of dielectric boundary points 50951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.220000 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) : 1.828673 object centre at (A) : 20.05550 28.39100 17.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4864706E-02 1.4643882E-02 midg,1,midg; midg,igrid,midg 3.8792688E-02 5.5212554E-02 1,midg,midg; igrid,midg,midg 0.4822910 0.3138327 gauss-seidel spectral radius is 0.9991898 estimated iterations to convergence 277 setup time was (sec) 1.400000 now iterating at: 09:25:42 rms-change max change #iterations 7.982976 433.7289 at 10iterations 4.510874 136.0626 at 20iterations 2.540345 68.82763 at 30iterations 1.418124 32.63378 at 40iterations 0.7961872 18.93863 at 50iterations 0.4442346 10.20058 at 60iterations 0.2476612 5.461224 at 70iterations 0.1385675 2.965610 at 80iterations 7.7325597E-02 1.591834 at 90iterations 4.3188360E-02 0.9708900 at 100iterations 2.4095427E-02 0.5188050 at 110iterations 1.3469134E-02 0.2847848 at 120iterations 7.5010555E-03 0.1700134 at 130iterations 4.2112614E-03 0.1058636 at 140iterations 2.3480845E-03 5.0200939E-02 at 150iterations 1.3079561E-03 2.6592255E-02 at 160iterations 7.3046994E-04 1.4909744E-02 at 170iterations 4.0933790E-04 8.8346004E-03 at 180iterations finished qdiffx linear iterations at : 09:25:57 total time elapsed so far: 16.44000 # loops : 180 mean,max change (kT/e) : 4.0933790E-04 8.8346004E-03 energy calculations done at 16.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.61000 DelPhi exited at 09:25:58 16.614u 0.446s 0:17.35 98.2% 0+0k 0+0io 0pf+0w