Sat Oct 8 16:35:32 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 Sat Oct 8 2011 at 16:35:32 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4574 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5425507 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): 17.05300 80.03200 ymin,ymax (A): 119.7130 185.3290 zmin,zma (A): -1.845000 59.82500 x,y,z range (A): 62.97900 65.61599 61.67000 scale (grids/A): 0.5425507 object centre (A): 48.54250 152.5210 28.99000 number of atom coordinates read : 4574 total number of charged atoms : 4385 net assigned charge : 2.906037 assigned positive charge : 701.0197 centred at (gu) : 91.67808 89.26148 87.32565 assigned negative charge : -698.1171 centred at (gu) : 91.63523 89.17902 87.34276 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8840 nv = 96 ne = 84 npr = 90478 no. pairs analyzed = 90478 no. exposed pairs = 5623 no. arc points = 39268 no. surface atoms = 1894 nbur = 2680 mkacc time = 0.2600000 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= 408 mr = 4761 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.5300000 number of dielectric boundary points 4467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4062 ## 554 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11631 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9705041E-10 1.1941960E-13 midg,1,midg; midg,igrid,midg -7.2977707E-10 7.3899376E-10 1,midg,midg; igrid,midg,midg -1.5509863E-10 8.1857104E-10 gauss-seidel spectral radius is 0.9826107 estimated iterations to convergence 62 setup time was (sec) 0.7900000 now iterating at: 16:35:33 rms-change max change #iterations 8.9203909E-02 15.09476 at 10iterations 6.2543852E-03 0.8612256 at 20iterations 6.6745596E-04 9.1629982E-02 at 30iterations 1.6181215E-04 2.1218777E-02 at 40iterations 4.9514147E-05 7.0457458E-03 at 50iterations finished qdiffx linear iterations at : 16:35:36 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 4.9514147E-05 7.0457458E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 16:35:37 4.261u 0.275s 0:04.84 93.5% 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 8 2011 at 16:35:37 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4574 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.627652 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): 17.05300 80.03200 ymin,ymax (A): 119.7130 185.3290 zmin,zma (A): -1.845000 59.82500 x,y,z range (A): 62.97900 65.61599 61.67000 scale (grids/A): 1.627652 object centre (A): 48.54250 152.5210 28.99000 number of atom coordinates read : 4574 total number of charged atoms : 4385 net assigned charge : 2.906037 assigned positive charge : 701.0197 centred at (gu) : 95.03283 87.78359 81.97590 assigned negative charge : -698.1171 centred at (gu) : 94.90546 87.53688 82.02767 start vw surface at 0.2000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 99194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39268 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 32057 mr = 69327 m= 3653 mr = 22304 m= 111 mr = 1938 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 447 time to turn everything in is 0.8600000 number of dielectric boundary points 41433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 525 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 33578 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) : 0.5425507 object centre at (A) : 48.54250 152.5210 28.99000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5269732E-03 8.3430838E-03 midg,1,midg; midg,igrid,midg 1.4514107E-02 3.2350104E-02 1,midg,midg; igrid,midg,midg -1.1085249E-02 -1.4795735E-02 gauss-seidel spectral radius is 0.9983326 estimated iterations to convergence 194 setup time was (sec) 1.170000 now iterating at: 16:35:38 rms-change max change #iterations 4.272327 194.4668 at 10iterations 1.842828 70.40373 at 20iterations 0.7927908 34.65789 at 30iterations 0.3438787 10.63998 at 40iterations 0.1484339 4.452484 at 50iterations 6.4492024E-02 2.011869 at 60iterations 2.7924087E-02 0.9000373 at 70iterations 1.2133722E-02 0.3628788 at 80iterations 5.2730870E-03 0.1626434 at 90iterations 2.3115345E-03 6.7565918E-02 at 100iterations 1.0248652E-03 3.1858444E-02 at 110iterations 4.6819661E-04 1.5362263E-02 at 120iterations finished qdiffx linear iterations at : 16:35:47 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 4.6819661E-04 1.5362263E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 16:35:47 9.801u 0.292s 0:10.41 96.9% 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 8 2011 at 16:35:47 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4574 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.441478 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): 17.05300 80.03200 ymin,ymax (A): 119.7130 185.3290 zmin,zma (A): -1.845000 59.82500 x,y,z range (A): 62.97900 65.61599 61.67000 scale (grids/A): 2.441478 object centre (A): 48.54250 152.5210 28.99000 number of atom coordinates read : 4574 total number of charged atoms : 4385 net assigned charge : 2.906037 assigned positive charge : 701.0197 centred at (gu) : 97.54916 86.67504 77.96349 assigned negative charge : -698.1171 centred at (gu) : 97.35806 86.30505 78.04155 start vw surface at 0.2100000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 230509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39268 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 110590 mr = 169218 m= 32926 mr = 88554 m= 5853 mr = 24983 m= 477 mr = 4005 m= 6 mr = 227 m= 0 mr = 2 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 1258 time to turn everything in is 2.150000 number of dielectric boundary points 93372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 35030 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) : 1.627652 object centre at (A) : 48.54250 152.5210 28.99000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1106564E-02 0.1831168 midg,1,midg; midg,igrid,midg 0.2264822 0.6131873 1,midg,midg; igrid,midg,midg -0.1562289 -0.2579664 gauss-seidel spectral radius is 0.9992134 estimated iterations to convergence 281 setup time was (sec) 2.490000 now iterating at: 16:35:50 rms-change max change #iterations 11.06442 437.9637 at 10iterations 6.404923 173.5224 at 20iterations 3.681314 79.15379 at 30iterations 2.108766 40.45809 at 40iterations 1.206209 22.47881 at 50iterations 0.6871948 12.04877 at 60iterations 0.3896982 7.316963 at 70iterations 0.2213238 4.094107 at 80iterations 0.1252455 2.208117 at 90iterations 7.0955366E-02 1.217262 at 100iterations 4.0180136E-02 0.7217598 at 110iterations 2.2703225E-02 0.3926778 at 120iterations 1.2859154E-02 0.2188711 at 130iterations 7.2662230E-03 0.1338463 at 140iterations 4.1102190E-03 7.3517799E-02 at 150iterations 2.3243793E-03 4.2976379E-02 at 160iterations 1.3142208E-03 2.3059845E-02 at 170iterations 7.4468157E-04 1.2387276E-02 at 180iterations finished qdiffx linear iterations at : 16:36:04 total time elapsed so far: 16.71000 # loops : 180 mean,max change (kT/e) : 7.4468157E-04 1.2387276E-02 energy calculations done at 16.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.89000 DelPhi exited at 16:36:05 16.887u 0.310s 0:17.48 98.3% 0+0k 0+0io 0pf+0w