Sun Oct 9 10:35:15 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 Sun Oct 9 2011 at 10:35:15 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 = 2644 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: 0.6325403 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): -13.81500 42.46600 ymin,ymax (A): 17.11400 71.28600 zmin,zma (A): -3.520000 47.48100 x,y,z range (A): 56.28100 54.17200 51.00100 scale (grids/A): 0.6325403 object centre (A): 14.32550 44.20000 21.98050 number of atom coordinates read : 2644 total number of charged atoms : 2500 net assigned charge : -3.499982 assigned positive charge : 381.4925 centred at (gu) : 90.99312 90.35663 91.72331 assigned negative charge : -384.9937 centred at (gu) : 90.96716 90.30336 91.78287 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7458 nv = 96 ne = 84 npr = 52601 no. pairs analyzed = 52601 no. exposed pairs = 3526 no. arc points = 24900 no. surface atoms = 1191 nbur = 1453 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3949 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.1900000 number of dielectric boundary points 3889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2299 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8658 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9235420E-10 -1.4041562E-08 midg,1,midg; midg,igrid,midg -8.3802263E-09 1.0408655E-09 1,midg,midg; igrid,midg,midg -5.2370992E-09 -1.9276603E-09 gauss-seidel spectral radius is 0.9870710 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 10:35:15 rms-change max change #iterations 0.1356894 23.69211 at 10iterations 1.3256350E-02 2.278618 at 20iterations 1.3278192E-03 0.2439804 at 30iterations 2.5462854E-04 3.7030458E-02 at 40iterations 1.2173065E-04 1.9463062E-02 at 50iterations finished qdiffx linear iterations at : 10:35:18 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.2173065E-04 1.9463062E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 10:35:18 3.341u 0.176s 0:03.87 90.6% 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 Sun Oct 9 2011 at 10:35:18 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 = 2644 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: 1.897621 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): -13.81500 42.46600 ymin,ymax (A): 17.11400 71.28600 zmin,zma (A): -3.520000 47.48100 x,y,z range (A): 56.28100 54.17200 51.00100 scale (grids/A): 1.897621 object centre (A): 14.32550 44.20000 21.98050 number of atom coordinates read : 2644 total number of charged atoms : 2500 net assigned charge : -3.499982 assigned positive charge : 381.4925 centred at (gu) : 92.97866 91.06927 95.16939 assigned negative charge : -384.9937 centred at (gu) : 92.90144 90.91006 95.34845 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24900 grid for indexing accessible points = 1.400000 m= 28149 mr = 54396 m= 4631 mr = 20025 m= 294 mr = 2761 m= 3 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 35871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19694 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) : 0.6325403 object centre at (A) : 14.32550 44.20000 21.98050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4874993E-02 7.9759983E-03 midg,1,midg; midg,igrid,midg -3.8248342E-02 -1.5103372E-02 1,midg,midg; igrid,midg,midg 7.2226315E-03 2.3899352E-02 gauss-seidel spectral radius is 0.9986523 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 10:35:19 rms-change max change #iterations 4.196491 196.2406 at 10iterations 1.962576 67.06389 at 20iterations 0.9244675 28.64037 at 30iterations 0.4331652 13.99833 at 40iterations 0.2039816 6.088364 at 50iterations 9.5826633E-02 3.176193 at 60iterations 4.5043852E-02 1.402145 at 70iterations 2.1270864E-02 0.6249313 at 80iterations 1.0000414E-02 0.3817673 at 90iterations 4.7273515E-03 0.1507578 at 100iterations 2.2548661E-03 6.8913698E-02 at 110iterations 1.0861417E-03 4.2248249E-02 at 120iterations finished qdiffx linear iterations at : 10:35:26 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.0861417E-03 4.2248249E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 10:35:27 7.753u 0.198s 0:08.32 95.4% 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 Sun Oct 9 2011 at 10:35:27 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 = 2644 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: 2.846431 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): -13.81500 42.46600 ymin,ymax (A): 17.11400 71.28600 zmin,zma (A): -3.520000 47.48100 x,y,z range (A): 56.28100 54.17200 51.00100 scale (grids/A): 2.846431 object centre (A): 14.32550 44.20000 21.98050 number of atom coordinates read : 2644 total number of charged atoms : 2500 net assigned charge : -3.499982 assigned positive charge : 381.4925 centred at (gu) : 94.46777 91.60377 97.75384 assigned negative charge : -384.9937 centred at (gu) : 94.35215 91.36501 98.02264 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 185306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24900 grid for indexing accessible points = 1.400000 m= 91045 mr = 132568 m= 32894 mr = 72555 m= 8294 mr = 25793 m= 1244 mr = 6129 m= 56 mr = 766 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 81023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 19995 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) : 1.897621 object centre at (A) : 14.32550 44.20000 21.98050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1444171 0.2270919 midg,1,midg; midg,igrid,midg -0.4090989 -0.1222578 1,midg,midg; igrid,midg,midg 0.1075027 0.4019152 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 1.260000 now iterating at: 10:35:28 rms-change max change #iterations 10.02165 335.1033 at 10iterations 5.963578 123.9954 at 20iterations 3.526615 73.64188 at 30iterations 2.074686 40.12180 at 40iterations 1.214692 26.59645 at 50iterations 0.7102782 12.55285 at 60iterations 0.4144865 7.031864 at 70iterations 0.2415716 4.335073 at 80iterations 0.1404931 2.531361 at 90iterations 8.1285894E-02 1.460231 at 100iterations 4.7287781E-02 0.8551483 at 110iterations 2.7442066E-02 0.5116367 at 120iterations 1.5943205E-02 0.2886276 at 130iterations 9.2287837E-03 0.1637111 at 140iterations 5.3655193E-03 0.1154709 at 150iterations 3.1094498E-03 5.9734732E-02 at 160iterations 1.8113916E-03 3.2665495E-02 at 170iterations 1.0649248E-03 1.9529343E-02 at 180iterations finished qdiffx linear iterations at : 10:35:40 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.0649248E-03 1.9529343E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 10:35:40 12.946u 0.216s 0:13.53 97.1% 0+0k 0+0io 0pf+0w