Tue Oct 11 08:00:12 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 08:00:12 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 = 2356 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: 0.6956930 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): -22.22800 21.39800 ymin,ymax (A): -59.39200 -8.220000 zmin,zma (A): -24.32400 24.83500 x,y,z range (A): 43.62600 51.17200 49.15900 scale (grids/A): 0.6956930 object centre (A): -0.4149990 -33.80600 0.2554998 number of atom coordinates read : 2356 total number of charged atoms : 2221 net assigned charge : 6.000006 assigned positive charge : 353.8283 centred at (gu) : 89.63084 89.90719 89.46469 assigned negative charge : -347.8288 centred at (gu) : 89.41210 89.89443 89.36903 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7694 nv = 96 ne = 84 npr = 47628 no. pairs analyzed = 47628 no. exposed pairs = 2841 no. arc points = 20242 no. surface atoms = 954 nbur = 1402 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4326 m= 4 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3100000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1909 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3329845E-09 7.1059702E-08 midg,1,midg; midg,igrid,midg 3.4137216E-08 4.3529187E-08 1,midg,midg; igrid,midg,midg -6.0014528E-08 1.2013365E-07 gauss-seidel spectral radius is 0.9892622 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 08:00:13 rms-change max change #iterations 0.2008442 25.65918 at 10iterations 2.4063643E-02 3.174116 at 20iterations 2.8239426E-03 0.3726387 at 30iterations 3.4397541E-04 4.9951553E-02 at 40iterations 4.0541883E-05 5.0449371E-03 at 50iterations finished qdiffx linear iterations at : 08:00:16 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 4.0541883E-05 5.0449371E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 08:00:16 3.452u 0.160s 0:03.93 91.8% 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 Tue Oct 11 2011 at 08:00:16 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 = 2356 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: 2.087079 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): -22.22800 21.39800 ymin,ymax (A): -59.39200 -8.220000 zmin,zma (A): -24.32400 24.83500 x,y,z range (A): 43.62600 51.17200 49.15900 scale (grids/A): 2.087079 object centre (A): -0.4149990 -33.80600 0.2554998 number of atom coordinates read : 2356 total number of charged atoms : 2221 net assigned charge : 6.000006 assigned positive charge : 353.8283 centred at (gu) : 88.89219 89.72107 88.39370 assigned negative charge : -347.8288 centred at (gu) : 88.23609 89.68330 88.10677 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20242 grid for indexing accessible points = 1.400000 m= 31963 mr = 56793 m= 5996 mr = 24353 m= 521 mr = 3964 m= 15 mr = 265 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 908 time to turn everything in is 0.6300000 number of dielectric boundary points 34602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17620 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) : 0.6956930 object centre at (A) : -0.4149990 -33.80600 0.2554998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4577888E-02 3.3509124E-02 midg,1,midg; midg,igrid,midg 2.3906311E-02 5.4601453E-02 1,midg,midg; igrid,midg,midg -2.5805458E-02 4.9960703E-02 gauss-seidel spectral radius is 0.9988272 estimated iterations to convergence 231 setup time was (sec) 0.9400000 now iterating at: 08:00:17 rms-change max change #iterations 4.744989 214.4625 at 10iterations 2.342132 74.61040 at 20iterations 1.158628 38.91300 at 30iterations 0.5739612 16.94381 at 40iterations 0.2838937 8.333595 at 50iterations 0.1407217 4.239876 at 60iterations 6.9515541E-02 2.203143 at 70iterations 3.4492657E-02 0.9598579 at 80iterations 1.7105410E-02 0.5019321 at 90iterations 8.4542045E-03 0.2581024 at 100iterations 4.1994993E-03 0.1302338 at 110iterations 2.0773308E-03 5.8908463E-02 at 120iterations finished qdiffx linear iterations at : 08:00:24 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 2.0773308E-03 5.8908463E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 08:00:25 8.132u 0.207s 0:08.91 93.4% 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 Tue Oct 11 2011 at 08:00:25 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 = 2356 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: 3.130618 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): -22.22800 21.39800 ymin,ymax (A): -59.39200 -8.220000 zmin,zma (A): -24.32400 24.83500 x,y,z range (A): 43.62600 51.17200 49.15900 scale (grids/A): 3.130618 object centre (A): -0.4149990 -33.80600 0.2554998 number of atom coordinates read : 2356 total number of charged atoms : 2221 net assigned charge : 6.000006 assigned positive charge : 353.8283 centred at (gu) : 88.33820 89.58158 87.59048 assigned negative charge : -347.8288 centred at (gu) : 87.35398 89.52486 87.16019 start vw surface at 0.1500000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 187688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20242 grid for indexing accessible points = 1.400000 m= 99779 mr = 136771 m= 40254 mr = 83024 m= 11313 mr = 33176 m= 2121 mr = 8776 m= 233 mr = 1522 m= 7 mr = 132 m= 0 mr = 3 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2816 time to turn everything in is 2.010000 number of dielectric boundary points 77991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 17766 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) : 2.087079 object centre at (A) : -0.4149990 -33.80600 0.2554998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4415798 0.2545690 midg,1,midg; midg,igrid,midg 4.3976057E-02 0.4264898 1,midg,midg; igrid,midg,midg -0.1876652 0.3678575 gauss-seidel spectral radius is 0.9992978 estimated iterations to convergence 298 setup time was (sec) 2.330000 now iterating at: 08:00:28 rms-change max change #iterations 10.56966 421.3258 at 10iterations 6.190663 126.7819 at 20iterations 3.628263 63.02626 at 30iterations 2.124763 39.02420 at 40iterations 1.243282 23.14229 at 50iterations 0.7266898 12.71386 at 60iterations 0.4239231 7.177117 at 70iterations 0.2469462 4.113796 at 80iterations 0.1442810 2.465961 at 90iterations 8.4178455E-02 1.554223 at 100iterations 4.9168382E-02 0.8411574 at 110iterations 2.8620649E-02 0.4698505 at 120iterations 1.6732639E-02 0.2804747 at 130iterations 9.7687859E-03 0.1738205 at 140iterations 5.7119769E-03 9.1581345E-02 at 150iterations 3.3461479E-03 5.6335449E-02 at 160iterations 1.9602685E-03 3.3859253E-02 at 170iterations 1.1546753E-03 1.9485474E-02 at 180iterations finished qdiffx linear iterations at : 08:00:39 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 1.1546753E-03 1.9485474E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.66000 DelPhi exited at 08:00:39 13.658u 0.206s 0:14.16 97.8% 0+0k 0+0io 0pf+0w