Tue Oct 11 04:19:02 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 Tue Oct 11 2011 at 04:19:02 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 = 2695 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: 0.6827379 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): -14.78200 33.27000 ymin,ymax (A): 7.424000 55.58000 zmin,zma (A): 25.73700 77.88000 x,y,z range (A): 48.05200 48.15600 52.14300 scale (grids/A): 0.6827379 object centre (A): 9.244000 31.50200 51.80850 number of atom coordinates read : 2695 total number of charged atoms : 2548 net assigned charge : 3.500014 assigned positive charge : 408.5497 centred at (gu) : 89.97887 90.55342 88.96461 assigned negative charge : -405.0504 centred at (gu) : 90.22997 90.37601 88.97995 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8449 nv = 96 ne = 84 npr = 55497 no. pairs analyzed = 55497 no. exposed pairs = 3259 no. arc points = 22573 no. surface atoms = 1092 nbur = 1603 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 521 mr = 4895 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3000000 number of dielectric boundary points 3991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2073 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9701 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6247999E-08 8.4522354E-09 midg,1,midg; midg,igrid,midg -4.4223793E-08 8.8400952E-08 1,midg,midg; igrid,midg,midg 1.0496078E-07 -7.7236763E-08 gauss-seidel spectral radius is 0.9888824 estimated iterations to convergence 77 setup time was (sec) 0.5200000 now iterating at: 04:19:03 rms-change max change #iterations 0.1982484 27.19289 at 10iterations 2.2726651E-02 2.896194 at 20iterations 2.6691875E-03 0.3150673 at 30iterations 3.2634626E-04 4.6211243E-02 at 40iterations 4.6288318E-05 6.5116882E-03 at 50iterations finished qdiffx linear iterations at : 04:19:05 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 4.6288318E-05 6.5116882E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 04:19:06 3.132u 0.135s 0:03.94 82.7% 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 Tue Oct 11 2011 at 04:19:06 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 = 2695 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.048214 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): -14.78200 33.27000 ymin,ymax (A): 7.424000 55.58000 zmin,zma (A): 25.73700 77.88000 x,y,z range (A): 48.05200 48.15600 52.14300 scale (grids/A): 2.048214 object centre (A): 9.244000 31.50200 51.80850 number of atom coordinates read : 2695 total number of charged atoms : 2548 net assigned charge : 3.500014 assigned positive charge : 408.5497 centred at (gu) : 89.93623 91.65976 86.89309 assigned negative charge : -405.0504 centred at (gu) : 90.68973 91.12768 86.93939 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22573 grid for indexing accessible points = 1.400000 m= 35019 mr = 64786 m= 6128 mr = 26591 m= 468 mr = 3979 m= 13 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1168 time to turn everything in is 0.6200000 number of dielectric boundary points 36618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20200 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) : 0.6827379 object centre at (A) : 9.244000 31.50200 51.80850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3365535E-02 8.9382622E-03 midg,1,midg; midg,igrid,midg -2.0543577E-02 4.1947562E-02 1,midg,midg; igrid,midg,midg 9.4826989E-02 -1.7435279E-02 gauss-seidel spectral radius is 0.9988185 estimated iterations to convergence 230 setup time was (sec) 0.8800000 now iterating at: 04:19:07 rms-change max change #iterations 5.017915 234.1125 at 10iterations 2.476787 88.75580 at 20iterations 1.225739 35.72334 at 30iterations 0.6066084 16.13475 at 40iterations 0.3004997 8.551810 at 50iterations 0.1484642 4.286963 at 60iterations 7.3622622E-02 2.107698 at 70iterations 3.6436446E-02 0.9936352 at 80iterations 1.8031454E-02 0.5217800 at 90iterations 8.9240540E-03 0.2679939 at 100iterations 4.4240737E-03 0.1249132 at 110iterations 2.2033046E-03 6.2388420E-02 at 120iterations finished qdiffx linear iterations at : 04:19:13 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 2.2033046E-03 6.2388420E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 04:19:14 7.105u 0.182s 0:07.81 93.2% 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 Tue Oct 11 2011 at 04:19:14 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 = 2695 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.072320 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): -14.78200 33.27000 ymin,ymax (A): 7.424000 55.58000 zmin,zma (A): 25.73700 77.88000 x,y,z range (A): 48.05200 48.15600 52.14300 scale (grids/A): 3.072320 object centre (A): 9.244000 31.50200 51.80850 number of atom coordinates read : 2695 total number of charged atoms : 2548 net assigned charge : 3.500014 assigned positive charge : 408.5497 centred at (gu) : 89.90417 92.48972 85.33975 assigned negative charge : -405.0504 centred at (gu) : 91.03430 91.69157 85.40913 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 209179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22573 grid for indexing accessible points = 1.400000 m= 111427 mr = 155956 m= 42969 mr = 93088 m= 11303 mr = 35310 m= 1994 mr = 8659 m= 178 mr = 1387 m= 6 mr = 89 m= 0 mr = 4 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 3787 time to turn everything in is 1.610000 number of dielectric boundary points 82563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 20384 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) : 2.048214 object centre at (A) : 9.244000 31.50200 51.80850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3483350 1.8945888E-02 midg,1,midg; midg,igrid,midg -0.1919546 0.4878444 1,midg,midg; igrid,midg,midg 0.7429331 -0.1022767 gauss-seidel spectral radius is 0.9993001 estimated iterations to convergence 298 setup time was (sec) 1.890000 now iterating at: 04:19:16 rms-change max change #iterations 11.22860 481.9791 at 10iterations 6.601624 130.5447 at 20iterations 3.889756 69.75318 at 30iterations 2.284953 39.36004 at 40iterations 1.339821 21.94245 at 50iterations 0.7869906 13.86502 at 60iterations 0.4612875 8.038511 at 70iterations 0.2704227 4.495931 at 80iterations 0.1583777 2.666361 at 90iterations 9.2676371E-02 1.442575 at 100iterations 5.4329142E-02 0.8722019 at 110iterations 3.1831458E-02 0.5564675 at 120iterations 1.8619332E-02 0.2903900 at 130iterations 1.0927594E-02 0.1841888 at 140iterations 6.4313854E-03 0.1020985 at 150iterations 3.8186542E-03 6.2017441E-02 at 160iterations 2.2834437E-03 4.2434692E-02 at 170iterations 1.3910965E-03 2.5175095E-02 at 180iterations finished qdiffx linear iterations at : 04:19:25 total time elapsed so far: 11.40000 # loops : 180 mean,max change (kT/e) : 1.3910965E-03 2.5175095E-02 energy calculations done at 11.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 04:19:26 11.559u 0.194s 0:12.38 94.8% 0+0k 0+0io 0pf+0w