Sat Oct 8 11:35:03 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 8 2011 at 11:35:03 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4362 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5355155 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): 59.82900 115.3300 ymin,ymax (A): 19.66500 81.52000 zmin,zma (A): -10.28500 56.19300 x,y,z range (A): 55.50100 61.85500 66.47800 scale (grids/A): 0.5355155 object centre (A): 87.57950 50.59250 22.95400 number of atom coordinates read : 4362 total number of charged atoms : 4203 net assigned charge : -0.9999546 assigned positive charge : 655.3993 centred at (gu) : 89.45757 90.05704 90.12432 assigned negative charge : -656.4025 centred at (gu) : 89.64178 89.99615 89.98441 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7805 nv = 96 ne = 84 npr = 91997 no. pairs analyzed = 91997 no. exposed pairs = 5012 no. arc points = 33896 no. surface atoms = 1697 nbur = 2665 mkacc time = 0.1500000 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 = 1.624000 m= 307 mr = 4352 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.3100000 number of dielectric boundary points 3740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3514 ## 463 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.5585373E-10 8.8553298E-10 midg,1,midg; midg,igrid,midg -4.4580739E-10 3.5529235E-10 1,midg,midg; igrid,midg,midg 1.3081247E-09 -1.1239873E-09 gauss-seidel spectral radius is 0.9821232 estimated iterations to convergence 62 setup time was (sec) 0.5100000 now iterating at: 11:35:04 rms-change max change #iterations 8.1928216E-02 14.31561 at 10iterations 5.6977673E-03 0.7700768 at 20iterations 7.0081046E-04 9.5096588E-02 at 30iterations 1.8133414E-04 2.3706436E-02 at 40iterations 5.6769251E-05 8.4869862E-03 at 50iterations finished qdiffx linear iterations at : 11:35:07 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 5.6769251E-05 8.4869862E-03 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 11:35:08 3.824u 0.219s 0:04.70 85.7% 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 8 2011 at 11:35:08 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4362 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.606547 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): 59.82900 115.3300 ymin,ymax (A): 19.66500 81.52000 zmin,zma (A): -10.28500 56.19300 x,y,z range (A): 55.50100 61.85500 66.47800 scale (grids/A): 1.606547 object centre (A): 87.57950 50.59250 22.95400 number of atom coordinates read : 4362 total number of charged atoms : 4203 net assigned charge : -0.9999546 assigned positive charge : 655.3993 centred at (gu) : 88.37147 90.16985 90.37226 assigned negative charge : -656.4025 centred at (gu) : 88.92485 89.98811 89.95261 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 88329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33896 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27783 mr = 62952 m= 2864 mr = 19773 m= 76 mr = 1518 m= 0 mr = 6 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5629 time to turn everything in is 0.4300000 number of dielectric boundary points 34803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 428 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 32049 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) : 0.5355155 object centre at (A) : 87.57950 50.59250 22.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4428042E-02 1.7951798E-02 midg,1,midg; midg,igrid,midg -1.7644394E-02 2.5790930E-02 1,midg,midg; igrid,midg,midg 2.4439050E-02 -1.8421244E-02 gauss-seidel spectral radius is 0.9982548 estimated iterations to convergence 190 setup time was (sec) 0.6600000 now iterating at: 11:35:08 rms-change max change #iterations 4.013367 190.1069 at 10iterations 1.701894 57.56479 at 20iterations 0.7233158 24.85312 at 30iterations 0.3071676 9.425762 at 40iterations 0.1305229 3.847994 at 50iterations 5.5520404E-02 1.767868 at 60iterations 2.3738215E-02 0.7166519 at 70iterations 1.0122932E-02 0.3083687 at 80iterations 4.3770466E-03 0.1445879 at 90iterations 1.9215471E-03 6.4359665E-02 at 100iterations 8.7083195E-04 2.5955200E-02 at 110iterations 4.2176287E-04 1.4282227E-02 at 120iterations finished qdiffx linear iterations at : 11:35:16 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 4.2176287E-04 1.4282227E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 11:35:16 8.310u 0.245s 0:08.89 96.1% 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 Sat Oct 8 2011 at 11:35:17 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4362 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.409820 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): 59.82900 115.3300 ymin,ymax (A): 19.66500 81.52000 zmin,zma (A): -10.28500 56.19300 x,y,z range (A): 55.50100 61.85500 66.47800 scale (grids/A): 2.409820 object centre (A): 87.57950 50.59250 22.95400 number of atom coordinates read : 4362 total number of charged atoms : 4203 net assigned charge : -0.9999546 assigned positive charge : 655.3993 centred at (gu) : 87.55681 90.25447 90.55803 assigned negative charge : -656.4025 centred at (gu) : 88.38725 89.98221 89.92879 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 205851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33896 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 96826 mr = 153707 m= 27769 mr = 78348 m= 4453 mr = 21566 m= 271 mr = 2968 m= 2 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 19226 time to turn everything in is 1.070000 number of dielectric boundary points 78470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 33582 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) : 1.606547 object centre at (A) : 87.57950 50.59250 22.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1664375 0.3352262 midg,1,midg; midg,igrid,midg -0.4794964 0.5235487 1,midg,midg; igrid,midg,midg 0.4328881 -0.2591842 gauss-seidel spectral radius is 0.9991858 estimated iterations to convergence 277 setup time was (sec) 1.330000 now iterating at: 11:35:18 rms-change max change #iterations 10.45718 286.6839 at 10iterations 5.994956 132.7331 at 20iterations 3.409650 68.06720 at 30iterations 1.935197 35.84696 at 40iterations 1.094321 20.47799 at 50iterations 0.6168888 11.13638 at 60iterations 0.3480596 6.556310 at 70iterations 0.1958230 3.643954 at 80iterations 0.1098937 2.018374 at 90iterations 6.1728496E-02 1.110994 at 100iterations 3.4660455E-02 0.6410923 at 110iterations 1.9471887E-02 0.3534325 at 120iterations 1.0922261E-02 0.1967525 at 130iterations 6.1566713E-03 0.1068230 at 140iterations 3.4812998E-03 6.9337845E-02 at 150iterations 1.9834349E-03 3.9937019E-02 at 160iterations 1.1490398E-03 1.9714355E-02 at 170iterations 6.8073237E-04 1.4144897E-02 at 180iterations finished qdiffx linear iterations at : 11:35:30 total time elapsed so far: 13.45000 # loops : 180 mean,max change (kT/e) : 6.8073237E-04 1.4144897E-02 energy calculations done at 13.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 11:35:31 13.586u 0.220s 0:14.09 97.9% 0+0k 0+0io 0pf+0w