Mon Oct 10 14:13:16 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+sph.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 = amb.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 14:13:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7043090 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): -13.27600 35.90900 ymin,ymax (A): -20.55300 22.01900 zmin,zma (A): -9.378000 41.16800 x,y,z range (A): 49.18500 42.57200 50.54600 scale (grids/A): 0.7043090 object centre (A): 11.31650 0.7330008 15.89500 number of atom coordinates read : 2182 total number of charged atoms : 2046 net assigned charge : -0.4999887 assigned positive charge : 327.7245 centred at (gu) : 90.39597 89.59948 90.78284 assigned negative charge : -328.2250 centred at (gu) : 90.15981 89.71800 90.68070 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7394 nv = 96 ne = 84 npr = 44199 no. pairs analyzed = 44199 no. exposed pairs = 2699 no. arc points = 18903 no. surface atoms = 915 nbur = 1267 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4102 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.1700000 number of dielectric boundary points 3685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1704 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8135 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7023423E-08 5.1704081E-08 midg,1,midg; midg,igrid,midg 5.6263488E-08 -5.8224789E-08 1,midg,midg; igrid,midg,midg -1.1287633E-07 1.1581572E-07 gauss-seidel spectral radius is 0.9895082 estimated iterations to convergence 79 setup time was (sec) 0.3600000 now iterating at: 14:13:16 rms-change max change #iterations 0.2035379 33.01972 at 10iterations 2.4711695E-02 3.165725 at 20iterations 3.1730514E-03 0.4441094 at 30iterations 4.2053428E-04 5.3534508E-02 at 40iterations 6.7625580E-05 1.0345459E-02 at 50iterations finished qdiffx linear iterations at : 14:13:19 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.7625580E-05 1.0345459E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 14:13:20 3.300u 0.172s 0:03.96 87.6% 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 14:13:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.112927 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): -13.27600 35.90900 ymin,ymax (A): -20.55300 22.01900 zmin,zma (A): -9.378000 41.16800 x,y,z range (A): 49.18500 42.57200 50.54600 scale (grids/A): 2.112927 object centre (A): 11.31650 0.7330008 15.89500 number of atom coordinates read : 2182 total number of charged atoms : 2046 net assigned charge : -0.4999887 assigned positive charge : 327.7245 centred at (gu) : 91.18771 88.79801 92.34862 assigned negative charge : -328.2250 centred at (gu) : 90.47953 89.15421 92.04201 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18903 grid for indexing accessible points = 1.400000 m= 31364 mr = 54634 m= 5934 mr = 23512 m= 492 mr = 3946 m= 10 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 350 time to turn everything in is 0.3900000 number of dielectric boundary points 33875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16242 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) : 0.7043090 object centre at (A) : 11.31650 0.7330008 15.89500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2395437E-03 -4.7338307E-03 midg,1,midg; midg,igrid,midg 1.3782646E-02 -2.0388447E-02 1,midg,midg; igrid,midg,midg -2.1842221E-02 -1.7779127E-02 gauss-seidel spectral radius is 0.9988409 estimated iterations to convergence 232 setup time was (sec) 0.6000000 now iterating at: 14:13:20 rms-change max change #iterations 4.730937 228.7898 at 10iterations 2.324528 86.41412 at 20iterations 1.158253 39.06263 at 30iterations 0.5724373 16.36784 at 40iterations 0.2851324 8.631009 at 50iterations 0.1421154 3.889021 at 60iterations 7.0559479E-02 2.090610 at 70iterations 3.5028599E-02 1.044256 at 80iterations 1.7500581E-02 0.5099039 at 90iterations 8.7381853E-03 0.2525616 at 100iterations 4.3682489E-03 0.1410084 at 110iterations 2.1999497E-03 6.5261364E-02 at 120iterations finished qdiffx linear iterations at : 14:13:27 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 2.1999497E-03 6.5261364E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 14:13:28 7.653u 0.198s 0:08.25 95.0% 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 14:13:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2182 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.169390 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): -13.27600 35.90900 ymin,ymax (A): -20.55300 22.01900 zmin,zma (A): -9.378000 41.16800 x,y,z range (A): 49.18500 42.57200 50.54600 scale (grids/A): 3.169390 object centre (A): 11.31650 0.7330008 15.89500 number of atom coordinates read : 2182 total number of charged atoms : 2046 net assigned charge : -0.4999887 assigned positive charge : 327.7245 centred at (gu) : 91.78156 88.19707 93.52285 assigned negative charge : -328.2250 centred at (gu) : 90.71918 88.73132 93.06306 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 180680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18903 grid for indexing accessible points = 1.400000 m= 97293 mr = 131683 m= 39978 mr = 80558 m= 11239 mr = 32662 m= 2031 mr = 8588 m= 172 mr = 1460 m= 9 mr = 78 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1331 time to turn everything in is 1.190000 number of dielectric boundary points 76373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 16368 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) : 2.112927 object centre at (A) : 11.31650 0.7330008 15.89500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6936064E-02 -0.1244090 midg,1,midg; midg,igrid,midg 0.1187893 -0.1662528 1,midg,midg; igrid,midg,midg -0.1285132 -0.3166379 gauss-seidel spectral radius is 0.9993031 estimated iterations to convergence 299 setup time was (sec) 1.420000 now iterating at: 14:13:30 rms-change max change #iterations 10.60023 416.3511 at 10iterations 6.298488 155.2043 at 20iterations 3.753055 86.92563 at 30iterations 2.228575 49.35933 at 40iterations 1.316762 25.85555 at 50iterations 0.7760473 16.16265 at 60iterations 0.4586026 9.266180 at 70iterations 0.2689457 5.078323 at 80iterations 0.1581964 2.875530 at 90iterations 9.3061991E-02 1.610632 at 100iterations 5.4708201E-02 1.016532 at 110iterations 3.2188676E-02 0.6064911 at 120iterations 1.9013777E-02 0.3577652 at 130iterations 1.1309351E-02 0.1959076 at 140iterations 6.7820898E-03 0.1244049 at 150iterations 4.1285688E-03 8.1138611E-02 at 160iterations 2.5878998E-03 5.2997589E-02 at 170iterations 1.6841440E-03 3.4904480E-02 at 180iterations finished qdiffx linear iterations at : 14:13:41 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 1.6841440E-03 3.4904480E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 14:13:41 12.627u 0.207s 0:13.42 95.5% 0+0k 0+0io 0pf+0w