Mon Oct 10 14:01:49 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 14:01:49 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 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: 0.6966050 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): -14.05300 37.05200 ymin,ymax (A): -0.5680000 44.28300 zmin,zma (A): -6.713000 43.99200 x,y,z range (A): 51.10500 44.85100 50.70500 scale (grids/A): 0.6966050 object centre (A): 11.49950 21.85750 18.63950 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 373.4411 centred at (gu) : 91.00584 91.58643 89.94931 assigned negative charge : -369.9416 centred at (gu) : 91.20261 91.65506 89.91497 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7710 nv = 96 ne = 84 npr = 49271 no. pairs analyzed = 49271 no. exposed pairs = 2997 no. arc points = 20565 no. surface atoms = 1006 nbur = 1414 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4299 m= 3 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3200000 number of dielectric boundary points 3834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1933 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7221377E-09 3.9624197E-08 midg,1,midg; midg,igrid,midg 4.0706496E-08 -1.0537704E-08 1,midg,midg; igrid,midg,midg 9.2130982E-08 -8.2989395E-08 gauss-seidel spectral radius is 0.9892921 estimated iterations to convergence 79 setup time was (sec) 0.6200000 now iterating at: 14:01:50 rms-change max change #iterations 0.2085334 30.50607 at 10iterations 2.4937695E-02 3.646475 at 20iterations 3.0060725E-03 0.3710632 at 30iterations 3.8263496E-04 5.1862955E-02 at 40iterations 5.8327030E-05 7.8277588E-03 at 50iterations finished qdiffx linear iterations at : 14:01:54 total time elapsed so far: 4.580000 # loops : 50 mean,max change (kT/e) : 5.8327030E-05 7.8277588E-03 energy calculations done at 4.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 14:01:54 4.751u 0.379s 0:05.56 92.0% 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 Mon Oct 10 2011 at 14:01:54 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 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: 2.089815 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): -14.05300 37.05200 ymin,ymax (A): -0.5680000 44.28300 zmin,zma (A): -6.713000 43.99200 x,y,z range (A): 51.10500 44.85100 50.70500 scale (grids/A): 2.089815 object centre (A): 11.49950 21.85750 18.63950 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 373.4411 centred at (gu) : 93.01717 94.75893 89.84750 assigned negative charge : -369.9416 centred at (gu) : 93.60760 94.96493 89.74482 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20565 grid for indexing accessible points = 1.400000 m= 32519 mr = 56201 m= 6719 mr = 24542 m= 606 mr = 4607 m= 22 mr = 309 m= 0 mr = 6 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 376 time to turn everything in is 0.7100000 number of dielectric boundary points 35130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 18072 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) : 0.6966050 object centre at (A) : 11.49950 21.85750 18.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0484971E-02 3.1246915E-02 midg,1,midg; midg,igrid,midg 3.4277476E-02 1.4599991E-03 1,midg,midg; igrid,midg,midg 2.1482918E-02 -7.3023312E-02 gauss-seidel spectral radius is 0.9988329 estimated iterations to convergence 232 setup time was (sec) 1.020000 now iterating at: 14:01:56 rms-change max change #iterations 4.966970 221.3194 at 10iterations 2.457379 82.21326 at 20iterations 1.219662 40.24024 at 30iterations 0.6069268 19.09529 at 40iterations 0.3012076 8.893890 at 50iterations 0.1498863 4.175799 at 60iterations 7.4440271E-02 2.218090 at 70iterations 3.7013181E-02 1.072104 at 80iterations 1.8324582E-02 0.5706379 at 90iterations 9.1032581E-03 0.2668571 at 100iterations 4.5258855E-03 0.1390915 at 110iterations 2.2563133E-03 6.8356514E-02 at 120iterations finished qdiffx linear iterations at : 14:02:06 total time elapsed so far: 11.43000 # loops : 120 mean,max change (kT/e) : 2.2563133E-03 6.8356514E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 14:02:07 11.588u 0.444s 0:12.60 95.3% 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 14:02:07 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.134722 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): -14.05300 37.05200 ymin,ymax (A): -0.5680000 44.28300 zmin,zma (A): -6.713000 43.99200 x,y,z range (A): 51.10500 44.85100 50.70500 scale (grids/A): 3.134722 object centre (A): 11.49950 21.85750 18.63950 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 373.4411 centred at (gu) : 94.52574 97.13824 89.77129 assigned negative charge : -369.9416 centred at (gu) : 95.41140 97.44718 89.61722 start vw surface at 0.1100000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 186553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20565 grid for indexing accessible points = 1.400000 m= 99552 mr = 135468 m= 42087 mr = 82360 m= 12914 mr = 34631 m= 2516 mr = 10052 m= 294 mr = 1873 m= 16 mr = 204 m= 0 mr = 7 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 1283 time to turn everything in is 2.170000 number of dielectric boundary points 79337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 18224 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) : 2.089815 object centre at (A) : 11.49950 21.85750 18.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2617300 0.1769420 midg,1,midg; midg,igrid,midg 0.2789454 -8.5361548E-02 1,midg,midg; igrid,midg,midg 0.3827947 -0.6506281 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 2.510000 now iterating at: 14:02:10 rms-change max change #iterations 11.20111 521.0703 at 10iterations 6.638628 137.5777 at 20iterations 3.917612 81.68288 at 30iterations 2.311896 43.86697 at 40iterations 1.359329 23.99042 at 50iterations 0.7978454 14.06423 at 60iterations 0.4682524 8.515926 at 70iterations 0.2737123 4.712234 at 80iterations 0.1605886 3.040189 at 90iterations 9.3929164E-02 1.651916 at 100iterations 5.4826260E-02 0.8852991 at 110iterations 3.2143969E-02 0.5790386 at 120iterations 1.8775508E-02 0.3205662 at 130iterations 1.0981550E-02 0.1708221 at 140iterations 6.4276233E-03 0.1077738 at 150iterations 3.7712157E-03 6.5690994E-02 at 160iterations 2.2226754E-03 3.7349701E-02 at 170iterations 1.3194132E-03 2.2828579E-02 at 180iterations finished qdiffx linear iterations at : 14:02:28 total time elapsed so far: 20.04000 # loops : 180 mean,max change (kT/e) : 1.3194132E-03 2.2828579E-02 energy calculations done at 20.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.21000 DelPhi exited at 14:02:28 20.212u 0.475s 0:21.10 98.0% 0+0k 0+0io 0pf+0w