Mon Oct 10 17:01:19 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 17:01:20 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 0.5856997 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): -25.61400 32.46000 ymin,ymax (A): -8.680000 43.53500 zmin,zma (A): 6.628000 67.41000 x,y,z range (A): 58.07400 52.21500 60.78201 scale (grids/A): 0.5856997 object centre (A): 3.422999 17.42750 37.01900 number of atom coordinates read : 3202 total number of charged atoms : 3059 net assigned charge : -5.243956 assigned positive charge : 482.9945 centred at (gu) : 90.19615 88.54005 91.19924 assigned negative charge : -488.2399 centred at (gu) : 90.26730 88.39465 91.30528 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7297 nv = 96 ne = 84 npr = 64064 no. pairs analyzed = 64064 no. exposed pairs = 4211 no. arc points = 29648 no. surface atoms = 1410 nbur = 1792 mkacc time = 0.1100000 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 = 1.512000 m= 335 mr = 3766 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2300000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3040 ## 324 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9291 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3219392E-09 -5.8075025E-09 midg,1,midg; midg,igrid,midg -7.8446121E-09 2.0292850E-09 1,midg,midg; igrid,midg,midg 7.4075457E-10 -3.5061116E-09 gauss-seidel spectral radius is 0.9849765 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 17:01:20 rms-change max change #iterations 0.1096784 16.29179 at 10iterations 8.6572496E-03 1.287333 at 20iterations 6.9590588E-04 0.1095791 at 30iterations 6.1188126E-05 9.3574524E-03 at 40iterations 7.2187563E-06 1.3899803E-03 at 50iterations finished qdiffx linear iterations at : 17:01:23 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 7.2187563E-06 1.3899803E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 17:01:24 3.634u 0.261s 0:04.57 85.1% 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 Mon Oct 10 2011 at 17:01:24 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 1.757099 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): -25.61400 32.46000 ymin,ymax (A): -8.680000 43.53500 zmin,zma (A): 6.628000 67.41000 x,y,z range (A): 58.07400 52.21500 60.78201 scale (grids/A): 1.757099 object centre (A): 3.422999 17.42750 37.01900 number of atom coordinates read : 3202 total number of charged atoms : 3059 net assigned charge : -5.243956 assigned positive charge : 482.9945 centred at (gu) : 90.58755 85.61935 93.59670 assigned negative charge : -488.2399 centred at (gu) : 90.80153 85.18361 93.91538 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29648 grid for indexing accessible points = 1.400000 m= 25824 mr = 54135 m= 3105 mr = 17911 m= 121 mr = 1609 m= 0 mr = 23 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 461 time to turn everything in is 0.3800000 number of dielectric boundary points 35498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 23783 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) : 0.5856997 object centre at (A) : 3.422999 17.42750 37.01900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9589595E-02 1.0250397E-02 midg,1,midg; midg,igrid,midg -4.1178703E-02 3.4759685E-03 1,midg,midg; igrid,midg,midg 1.1391303E-02 -3.6725994E-02 gauss-seidel spectral radius is 0.9984646 estimated iterations to convergence 202 setup time was (sec) 0.6400000 now iterating at: 17:01:25 rms-change max change #iterations 4.091165 157.4166 at 10iterations 1.813416 57.68634 at 20iterations 0.8116033 27.27736 at 30iterations 0.3617172 10.99330 at 40iterations 0.1617763 5.502745 at 50iterations 7.2235197E-02 2.228858 at 60iterations 3.2297168E-02 1.082890 at 70iterations 1.4439358E-02 0.4662790 at 80iterations 6.4766151E-03 0.2179542 at 90iterations 2.8955441E-03 9.2182159E-02 at 100iterations 1.2995559E-03 4.7616959E-02 at 110iterations 5.8043079E-04 2.0769119E-02 at 120iterations finished qdiffx linear iterations at : 17:01:33 total time elapsed so far: 8.600000 # loops : 120 mean,max change (kT/e) : 5.8043079E-04 2.0769119E-02 energy calculations done at 8.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 17:01:34 8.733u 0.257s 0:09.51 94.4% 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 17:01:34 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: HIR 148 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 2.635648 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): -25.61400 32.46000 ymin,ymax (A): -8.680000 43.53500 zmin,zma (A): 6.628000 67.41000 x,y,z range (A): 58.07400 52.21500 60.78201 scale (grids/A): 2.635648 object centre (A): 3.422999 17.42750 37.01900 number of atom coordinates read : 3202 total number of charged atoms : 3059 net assigned charge : -5.243956 assigned positive charge : 482.9945 centred at (gu) : 90.88110 83.42877 95.39468 assigned negative charge : -488.2399 centred at (gu) : 91.20229 82.77515 95.87293 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29648 grid for indexing accessible points = 1.400000 m= 87107 mr = 132315 m= 27378 mr = 68804 m= 4989 mr = 20756 m= 452 mr = 3406 m= 19 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 1440 time to turn everything in is 1.020000 number of dielectric boundary points 80305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 24462 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) : 1.757099 object centre at (A) : 3.422999 17.42750 37.01900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5109934 0.2245710 midg,1,midg; midg,igrid,midg -0.4728873 4.4585757E-02 1,midg,midg; igrid,midg,midg 0.2519626 -0.4563201 gauss-seidel spectral radius is 0.9992328 estimated iterations to convergence 285 setup time was (sec) 1.300000 now iterating at: 17:01:35 rms-change max change #iterations 10.16939 309.4214 at 10iterations 5.936205 150.4086 at 20iterations 3.434162 73.86597 at 30iterations 1.978172 40.55967 at 40iterations 1.133860 24.65547 at 50iterations 0.6511638 14.46482 at 60iterations 0.3720726 7.510674 at 70iterations 0.2127841 4.135004 at 80iterations 0.1212970 2.299808 at 90iterations 6.8975449E-02 1.345411 at 100iterations 3.9258491E-02 0.7062378 at 110iterations 2.2372572E-02 0.4005718 at 120iterations 1.2768217E-02 0.2541790 at 130iterations 7.2309910E-03 0.1264820 at 140iterations 4.1219112E-03 7.7295303E-02 at 150iterations 2.3445806E-03 4.2451382E-02 at 160iterations 1.3332603E-03 2.4121761E-02 at 170iterations 7.5871643E-04 1.3633728E-02 at 180iterations finished qdiffx linear iterations at : 17:01:47 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 7.5871643E-04 1.3633728E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 17:01:48 13.331u 0.286s 0:14.04 96.9% 0+0k 0+0io 0pf+0w