Sat Oct 15 12:08:41 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 15 2011 at 12:08:41 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6618946 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): -0.4250001 53.36000 ymin,ymax (A): -16.16100 27.56100 zmin,zma (A): 32.69300 84.57899 x,y,z range (A): 53.78500 43.72200 51.88600 scale (grids/A): 0.6618946 object centre (A): 26.46750 5.700001 58.63599 number of atom coordinates read : 2255 total number of charged atoms : 2122 net assigned charge : 13.01401 assigned positive charge : 331.0134 centred at (gu) : 90.53042 89.41282 88.71003 assigned negative charge : -318.0002 centred at (gu) : 90.53526 89.43118 88.80778 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6886 nv = 96 ne = 84 npr = 44600 no. pairs analyzed = 44600 no. exposed pairs = 3027 no. arc points = 21434 no. surface atoms = 1010 nbur = 1245 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3638 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 90 time to turn everything in is 0.1800000 number of dielectric boundary points 3626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2035 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6378895E-08 1.3915791E-08 midg,1,midg; midg,igrid,midg 4.2335511E-08 2.7928193E-08 1,midg,midg; igrid,midg,midg 3.1770281E-08 3.7448604E-08 gauss-seidel spectral radius is 0.9881466 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 12:08:41 rms-change max change #iterations 0.1539940 21.81116 at 10iterations 1.6538851E-02 2.351497 at 20iterations 2.0347927E-03 0.2806797 at 30iterations 4.3717623E-04 6.4842224E-02 at 40iterations 1.4655745E-04 2.1356583E-02 at 50iterations finished qdiffx linear iterations at : 12:08:45 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 1.4655745E-04 2.1356583E-02 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 12:08:45 3.837u 0.230s 0:04.51 90.0% 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 15 2011 at 12:08:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.985684 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): -0.4250001 53.36000 ymin,ymax (A): -16.16100 27.56100 zmin,zma (A): 32.69300 84.57899 x,y,z range (A): 53.78500 43.72200 51.88600 scale (grids/A): 1.985684 object centre (A): 26.46750 5.700001 58.63599 number of atom coordinates read : 2255 total number of charged atoms : 2122 net assigned charge : 13.01401 assigned positive charge : 331.0134 centred at (gu) : 91.59082 88.23824 86.12991 assigned negative charge : -318.0002 centred at (gu) : 91.60593 88.29366 86.42337 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21434 grid for indexing accessible points = 1.400000 m= 27118 mr = 49487 m= 4880 mr = 19416 m= 408 mr = 3075 m= 4 mr = 151 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2008 time to turn everything in is 0.3900000 number of dielectric boundary points 33257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 16785 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) : 0.6618946 object centre at (A) : 26.46750 5.700001 58.63599 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4161708E-02 4.6001654E-02 midg,1,midg; midg,igrid,midg 3.3673715E-02 1.0281975E-02 1,midg,midg; igrid,midg,midg 4.7444258E-02 5.1851209E-02 gauss-seidel spectral radius is 0.9987157 estimated iterations to convergence 221 setup time was (sec) 0.6600000 now iterating at: 12:08:46 rms-change max change #iterations 4.178360 203.9635 at 10iterations 2.001312 68.03847 at 20iterations 0.9582407 35.35956 at 30iterations 0.4576041 14.20128 at 40iterations 0.2199201 6.971642 at 50iterations 0.1049387 3.449200 at 60iterations 5.0602548E-02 1.614197 at 70iterations 2.4165396E-02 0.7862463 at 80iterations 1.1741649E-02 0.3555164 at 90iterations 5.7607288E-03 0.1834087 at 100iterations 2.8973264E-03 0.1040020 at 110iterations 1.5361181E-03 5.2364349E-02 at 120iterations finished qdiffx linear iterations at : 12:08:54 total time elapsed so far: 8.570000 # loops : 120 mean,max change (kT/e) : 1.5361181E-03 5.2364349E-02 energy calculations done at 8.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.700000 DelPhi exited at 12:08:55 8.705u 0.290s 0:09.61 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 15 2011 at 12:08:55 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2255 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.978526 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): -0.4250001 53.36000 ymin,ymax (A): -16.16100 27.56100 zmin,zma (A): 32.69300 84.57899 x,y,z range (A): 53.78500 43.72200 51.88600 scale (grids/A): 2.978526 object centre (A): 26.46750 5.700001 58.63599 number of atom coordinates read : 2255 total number of charged atoms : 2122 net assigned charge : 13.01401 assigned positive charge : 331.0134 centred at (gu) : 92.38631 87.35732 84.19476 assigned negative charge : -318.0002 centred at (gu) : 92.40905 87.44051 84.63519 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 168284 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21434 grid for indexing accessible points = 1.400000 m= 85631 mr = 119833 m= 32864 mr = 68720 m= 9048 mr = 26095 m= 1597 mr = 6684 m= 145 mr = 1092 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 6495 time to turn everything in is 1.050000 number of dielectric boundary points 75086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 16976 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) : 1.985684 object centre at (A) : 26.46750 5.700001 58.63599 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8895896 0.6266033 midg,1,midg; midg,igrid,midg 0.2981580 4.6502918E-02 1,midg,midg; igrid,midg,midg 0.4469718 0.4202162 gauss-seidel spectral radius is 0.9992830 estimated iterations to convergence 295 setup time was (sec) 1.340000 now iterating at: 12:08:57 rms-change max change #iterations 9.751117 378.2679 at 10iterations 5.797506 125.3663 at 20iterations 3.432520 69.96755 at 30iterations 2.013299 39.44312 at 40iterations 1.185694 24.01699 at 50iterations 0.6925048 14.56868 at 60iterations 0.4054161 8.206533 at 70iterations 0.2366488 4.445261 at 80iterations 0.1381085 2.679947 at 90iterations 8.0627434E-02 1.506199 at 100iterations 4.6791498E-02 0.8644915 at 110iterations 2.7313193E-02 0.5474319 at 120iterations 1.5912689E-02 0.2899570 at 130iterations 9.2937574E-03 0.1900616 at 140iterations 5.4656300E-03 0.1049061 at 150iterations 3.2439446E-03 6.1496735E-02 at 160iterations 1.9624049E-03 3.9489746E-02 at 170iterations 1.2347713E-03 2.5745392E-02 at 180iterations finished qdiffx linear iterations at : 12:09:10 total time elapsed so far: 14.75000 # loops : 180 mean,max change (kT/e) : 1.2347713E-03 2.5745392E-02 energy calculations done at 14.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.88000 DelPhi exited at 12:09:11 14.877u 0.333s 0:15.71 96.7% 0+0k 0+0io 0pf+0w