Sat Oct 8 17:54:32 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 8 2011 at 17:54:32 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 = 4618 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4954422 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): -0.9610000 61.62000 ymin,ymax (A): -29.48800 31.26800 zmin,zma (A): -23.69700 48.15800 x,y,z range (A): 62.58100 60.75600 71.85500 scale (grids/A): 0.4954422 object centre (A): 30.32950 0.8899994 12.23050 number of atom coordinates read : 4618 total number of charged atoms : 4464 net assigned charge : -6.999970 assigned positive charge : 699.5791 centred at (gu) : 91.17028 91.16794 90.34543 assigned negative charge : -706.5839 centred at (gu) : 91.21553 91.16373 90.37682 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7262 nv = 96 ne = 84 npr = 90702 no. pairs analyzed = 90702 no. exposed pairs = 6170 no. arc points = 43380 no. surface atoms = 2054 nbur = 2564 mkacc time = 0.1900000 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 = 1.736000 m= 260 mr = 3512 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4223 ## 712 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9807 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9807471E-12 -9.8606172E-11 midg,1,midg; midg,igrid,midg -3.9739455E-11 -5.8461493E-11 1,midg,midg; igrid,midg,midg 7.1442513E-12 -1.4873858E-10 gauss-seidel spectral radius is 0.9791725 estimated iterations to convergence 57 setup time was (sec) 0.6700000 now iterating at: 17:54:33 rms-change max change #iterations 5.3445566E-02 9.875954 at 10iterations 2.9744897E-03 0.5153646 at 20iterations 3.2960851E-04 6.1418533E-02 at 30iterations 7.9094651E-05 1.5112877E-02 at 40iterations 2.1083100E-05 3.9882660E-03 at 50iterations finished qdiffx linear iterations at : 17:54:36 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 2.1083100E-05 3.9882660E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 17:54:36 3.518u 0.207s 0:03.99 92.9% 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 17:54:36 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 = 4618 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.486327 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): -0.9610000 61.62000 ymin,ymax (A): -29.48800 31.26800 zmin,zma (A): -23.69700 48.15800 x,y,z range (A): 62.58100 60.75600 71.85500 scale (grids/A): 1.486327 object centre (A): 30.32950 0.8899994 12.23050 number of atom coordinates read : 4618 total number of charged atoms : 4464 net assigned charge : -6.999970 assigned positive charge : 699.5791 centred at (gu) : 93.50956 93.50207 91.03502 assigned negative charge : -706.5839 centred at (gu) : 93.64589 93.49092 91.13004 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43380 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 22359 mr = 53674 m= 1691 mr = 14198 m= 34 mr = 612 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 37230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 715 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 33205 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) : 0.4954422 object centre at (A) : 30.32950 0.8899994 12.23050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0029182E-02 -1.8727925E-02 midg,1,midg; midg,igrid,midg -8.2882904E-03 -6.8681915E-03 1,midg,midg; igrid,midg,midg 3.5562876E-03 -6.2783191E-04 gauss-seidel spectral radius is 0.9979702 estimated iterations to convergence 177 setup time was (sec) 0.8900000 now iterating at: 17:54:37 rms-change max change #iterations 3.462714 142.4302 at 10iterations 1.370113 52.24711 at 20iterations 0.5416446 19.53601 at 30iterations 0.2157142 7.636078 at 40iterations 8.5577674E-02 2.875942 at 50iterations 3.3798419E-02 1.168411 at 60iterations 1.3493213E-02 0.4388533 at 70iterations 5.3682062E-03 0.1689796 at 80iterations 2.1500648E-03 7.4105263E-02 at 90iterations 8.6617935E-04 3.0746460E-02 at 100iterations 3.5750479E-04 1.3473511E-02 at 110iterations 1.5380372E-04 6.6471100E-03 at 120iterations finished qdiffx linear iterations at : 17:54:44 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.5380372E-04 6.6471100E-03 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 17:54:45 8.028u 0.252s 0:08.55 96.7% 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 17:54:45 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 = 4618 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.229490 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): -0.9610000 61.62000 ymin,ymax (A): -29.48800 31.26800 zmin,zma (A): -23.69700 48.15800 x,y,z range (A): 62.58100 60.75600 71.85500 scale (grids/A): 2.229490 object centre (A): 30.32950 0.8899994 12.23050 number of atom coordinates read : 4618 total number of charged atoms : 4464 net assigned charge : -6.999970 assigned positive charge : 699.5791 centred at (gu) : 95.26395 95.25264 91.55202 assigned negative charge : -706.5839 centred at (gu) : 95.46874 95.23639 91.69501 start vw surface at 0.1900000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 190143 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43380 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 81239 mr = 132479 m= 19117 mr = 61925 m= 2275 mr = 13213 m= 78 mr = 1238 m= 0 mr = 15 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 83982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 35579 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) : 1.486327 object centre at (A) : 30.32950 0.8899994 12.23050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1672227 -0.2973144 midg,1,midg; midg,igrid,midg -0.2577976 -0.1325031 1,midg,midg; igrid,midg,midg 3.6214165E-02 -5.5278882E-02 gauss-seidel spectral radius is 0.9991145 estimated iterations to convergence 265 setup time was (sec) 1.710000 now iterating at: 17:54:47 rms-change max change #iterations 9.671946 292.9168 at 10iterations 5.501627 150.3776 at 20iterations 3.094548 71.72729 at 30iterations 1.728062 45.96159 at 40iterations 0.9617747 21.97594 at 50iterations 0.5331331 12.29208 at 60iterations 0.2941911 6.520517 at 70iterations 0.1620205 3.606863 at 80iterations 8.9309238E-02 1.872253 at 90iterations 4.8946336E-02 0.9321612 at 100iterations 2.6923982E-02 0.5069866 at 110iterations 1.4717766E-02 0.3039627 at 120iterations 8.0777332E-03 0.1512346 at 130iterations 4.4305478E-03 8.9691162E-02 at 140iterations 2.4340714E-03 4.9764395E-02 at 150iterations 1.3402359E-03 2.6005030E-02 at 160iterations 7.4229075E-04 1.4659882E-02 at 170iterations 4.1367573E-04 8.5778236E-03 at 180iterations finished qdiffx linear iterations at : 17:54:58 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 4.1367573E-04 8.5778236E-03 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 17:54:58 13.241u 0.232s 0:13.75 97.9% 0+0k 0+0io 0pf+0w