Sat Oct 15 11:28:06 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 Sat Oct 15 2011 at 11:28:06 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 = 3366 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: 0.5438768 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): -15.17700 42.53400 ymin,ymax (A): -38.59800 26.85800 zmin,zma (A): -17.22800 34.09100 x,y,z range (A): 57.71100 65.45600 51.31900 scale (grids/A): 0.5438768 object centre (A): 13.67850 -5.870002 8.431499 number of atom coordinates read : 3366 total number of charged atoms : 3221 net assigned charge : -2.499994 assigned positive charge : 501.7385 centred at (gu) : 91.17292 91.64546 90.69038 assigned negative charge : -504.2399 centred at (gu) : 91.12963 91.64584 90.65688 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6316 nv = 96 ne = 84 npr = 68729 no. pairs analyzed = 68729 no. exposed pairs = 4052 no. arc points = 28377 no. surface atoms = 1373 nbur = 1993 mkacc time = 0.1200000 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 = 1.568000 m= 266 mr = 3403 m= 0 mr = 15 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2400000 number of dielectric boundary points 3164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2857 ## 400 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 8379 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2147190E-10 1.0018795E-10 midg,1,midg; midg,igrid,midg -9.8255550E-11 -2.2540322E-10 1,midg,midg; igrid,midg,midg -3.3658537E-10 2.0496475E-10 gauss-seidel spectral radius is 0.9825966 estimated iterations to convergence 62 setup time was (sec) 0.5200000 now iterating at: 11:28:07 rms-change max change #iterations 7.2894759E-02 13.77015 at 10iterations 4.8850281E-03 0.6859522 at 20iterations 3.4339048E-04 5.1858902E-02 at 30iterations 3.0104033E-05 6.8035126E-03 at 40iterations 3.7700140E-06 7.4100494E-04 at 50iterations finished qdiffx linear iterations at : 11:28:11 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 3.7700140E-06 7.4100494E-04 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 11:28:11 4.071u 0.295s 0:04.65 93.7% 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 15 2011 at 11:28:11 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 = 3366 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: 1.631630 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): -15.17700 42.53400 ymin,ymax (A): -38.59800 26.85800 zmin,zma (A): -17.22800 34.09100 x,y,z range (A): 57.71100 65.45600 51.31900 scale (grids/A): 1.631630 object centre (A): 13.67850 -5.870002 8.431499 number of atom coordinates read : 3366 total number of charged atoms : 3221 net assigned charge : -2.499994 assigned positive charge : 501.7385 centred at (gu) : 93.51781 94.93571 92.07035 assigned negative charge : -504.2399 centred at (gu) : 93.38845 94.93723 91.97041 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 71132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28377 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21731 mr = 49524 m= 2274 mr = 15294 m= 64 mr = 1094 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 568 time to turn everything in is 0.3900000 number of dielectric boundary points 29287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 315 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 24643 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) : 0.5438768 object centre at (A) : 13.67850 -5.870002 8.431499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5390126E-03 2.8230117E-03 midg,1,midg; midg,igrid,midg 4.6696565E-03 -2.6648613E-03 1,midg,midg; igrid,midg,midg -5.6736455E-03 -1.5199227E-03 gauss-seidel spectral radius is 0.9982128 estimated iterations to convergence 188 setup time was (sec) 0.7000000 now iterating at: 11:28:12 rms-change max change #iterations 3.517776 182.5993 at 10iterations 1.477834 57.62514 at 20iterations 0.6201151 22.37349 at 30iterations 0.2604432 8.973089 at 40iterations 0.1095177 4.255531 at 50iterations 4.6038698E-02 1.650589 at 60iterations 1.9454829E-02 0.7295609 at 70iterations 8.1393318E-03 0.2957077 at 80iterations 3.4321004E-03 0.1126981 at 90iterations 1.4477327E-03 5.0151825E-02 at 100iterations 6.1058841E-04 2.0687103E-02 at 110iterations 2.5796384E-04 8.6355209E-03 at 120iterations finished qdiffx linear iterations at : 11:28:24 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 2.5796384E-04 8.6355209E-03 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 11:28:25 9.310u 0.367s 0:13.45 71.8% 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 11:28:25 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 = 3366 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: 2.447446 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): -15.17700 42.53400 ymin,ymax (A): -38.59800 26.85800 zmin,zma (A): -17.22800 34.09100 x,y,z range (A): 57.71100 65.45600 51.31900 scale (grids/A): 2.447446 object centre (A): 13.67850 -5.870002 8.431499 number of atom coordinates read : 3366 total number of charged atoms : 3221 net assigned charge : -2.499994 assigned positive charge : 501.7385 centred at (gu) : 95.27640 97.40338 93.10532 assigned negative charge : -504.2399 centred at (gu) : 95.08262 97.40559 92.95538 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 165601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28377 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 76601 mr = 121072 m= 21319 mr = 61484 m= 3548 mr = 16162 m= 238 mr = 2311 m= 7 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 1791 time to turn everything in is 0.9000000 number of dielectric boundary points 66192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 25732 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) : 1.631630 object centre at (A) : 13.67850 -5.870002 8.431499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8897316E-02 6.5825500E-02 midg,1,midg; midg,igrid,midg 2.4707761E-02 8.3751418E-02 1,midg,midg; igrid,midg,midg -5.8764983E-02 1.3403472E-02 gauss-seidel spectral radius is 0.9991494 estimated iterations to convergence 271 setup time was (sec) 1.210000 now iterating at: 11:28:26 rms-change max change #iterations 9.049951 359.9323 at 10iterations 5.071556 124.6553 at 20iterations 2.835367 62.89595 at 30iterations 1.576050 31.23643 at 40iterations 0.8754671 18.16547 at 50iterations 0.4846835 10.29702 at 60iterations 0.2688737 5.310110 at 70iterations 0.1487384 2.983173 at 80iterations 8.1995487E-02 1.609167 at 90iterations 4.5247875E-02 0.9945498 at 100iterations 2.5038272E-02 0.5754776 at 110iterations 1.3831626E-02 0.3021373 at 120iterations 7.6383548E-03 0.1509748 at 130iterations 4.2171483E-03 8.0760002E-02 at 140iterations 2.3324182E-03 4.7580719E-02 at 150iterations 1.2867295E-03 2.5028229E-02 at 160iterations 7.1054499E-04 1.7917633E-02 at 170iterations 3.9364034E-04 8.6364746E-03 at 180iterations finished qdiffx linear iterations at : 11:28:39 total time elapsed so far: 13.95000 # loops : 180 mean,max change (kT/e) : 3.9364034E-04 8.6364746E-03 energy calculations done at 13.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.07000 DelPhi exited at 11:28:40 14.074u 0.301s 0:14.95 96.1% 0+0k 0+0io 0pf+0w