Tue Oct 11 08:00:40 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 Tue Oct 11 2011 at 08:00:40 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 !!! WARNING: HIR 57 has a net charge of 0.5140 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 : 6.014006 assigned positive charge : 357.0704 centred at (gu) : 89.64445 89.91236 89.41075 assigned negative charge : -351.0568 centred at (gu) : 89.42085 89.89738 89.31583 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 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 = 0.1100000 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 = 0.1300000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3200000 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 -2.3208799E-09 7.0473476E-08 midg,1,midg; midg,igrid,midg 3.3202365E-08 4.4666166E-08 1,midg,midg; igrid,midg,midg -6.2979673E-08 1.2318452E-07 gauss-seidel spectral radius is 0.9892622 estimated iterations to convergence 79 setup time was (sec) 0.5600000 now iterating at: 08:00:40 rms-change max change #iterations 0.2048144 26.26739 at 10iterations 2.4476102E-02 3.334028 at 20iterations 2.8858692E-03 0.3782921 at 30iterations 3.5014196E-04 5.3670883E-02 at 40iterations 4.1340722E-05 5.2680969E-03 at 50iterations finished qdiffx linear iterations at : 08:00:43 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.1340722E-05 5.2680969E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 08:00:44 3.527u 0.173s 0:04.05 91.1% 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 Tue Oct 11 2011 at 08:00:44 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 !!! WARNING: HIR 57 has a net charge of 0.5140 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: 2.087079 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 : 6.014006 assigned positive charge : 357.0704 centred at (gu) : 88.93303 89.73658 88.23189 assigned negative charge : -351.0568 centred at (gu) : 88.26233 89.69215 87.94717 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 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 = 0.3100000 no. cavity mid-points inaccessible to solvent = 908 time to turn everything in is 0.6500000 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 0.7800000 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 3.6040172E-02 3.3316728E-02 midg,1,midg; midg,igrid,midg 2.3071248E-02 5.4660022E-02 1,midg,midg; igrid,midg,midg -2.7219867E-02 5.1544100E-02 gauss-seidel spectral radius is 0.9988272 estimated iterations to convergence 231 setup time was (sec) 0.9600000 now iterating at: 08:00:45 rms-change max change #iterations 4.797377 214.4625 at 10iterations 2.367722 74.61038 at 20iterations 1.172122 38.91299 at 30iterations 0.5804556 16.92688 at 40iterations 0.2870612 8.311222 at 50iterations 0.1423268 4.316437 at 60iterations 7.0300810E-02 2.242056 at 70iterations 3.4879893E-02 0.9614677 at 80iterations 1.7297991E-02 0.5005884 at 90iterations 8.5487524E-03 0.2629585 at 100iterations 4.2465795E-03 0.1339283 at 110iterations 2.1004328E-03 5.9947968E-02 at 120iterations finished qdiffx linear iterations at : 08:00:52 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.1004328E-03 5.9947968E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 08:00:52 8.036u 0.209s 0:08.63 95.3% 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 08:00:52 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 !!! WARNING: HIR 57 has a net charge of 0.5140 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 : 6.014006 assigned positive charge : 357.0704 centred at (gu) : 88.39948 89.60485 87.34778 assigned negative charge : -351.0568 centred at (gu) : 87.39333 89.53812 86.92075 start vw surface at 0.1600000 fill in re-entrant regions at 0.9200000 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 = 0.9500000 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 2.170000 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 0.4727353 0.2528625 midg,1,midg; midg,igrid,midg 3.7616987E-02 0.4263192 1,midg,midg; igrid,midg,midg -0.1998000 0.3829519 gauss-seidel spectral radius is 0.9992978 estimated iterations to convergence 298 setup time was (sec) 2.350000 now iterating at: 08:00:55 rms-change max change #iterations 10.67944 421.3255 at 10iterations 6.254550 129.0328 at 20iterations 3.665880 63.35447 at 30iterations 2.147005 39.15722 at 40iterations 1.256058 23.21612 at 50iterations 0.7341170 12.96318 at 60iterations 0.4282110 7.264911 at 70iterations 0.2494458 4.119070 at 80iterations 0.1457162 2.486878 at 90iterations 8.5046098E-02 1.590800 at 100iterations 4.9683046E-02 0.8091683 at 110iterations 2.8916158E-02 0.4676461 at 120iterations 1.6912097E-02 0.2766151 at 130iterations 9.8770736E-03 0.1771622 at 140iterations 5.7814238E-03 9.2922211E-02 at 150iterations 3.3899650E-03 5.6898117E-02 at 160iterations 1.9903528E-03 3.4076691E-02 at 170iterations 1.1759867E-03 1.9439697E-02 at 180iterations finished qdiffx linear iterations at : 08:01:06 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 1.1759867E-03 1.9439697E-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) 13.65000 DelPhi exited at 08:01:07 13.650u 0.221s 0:14.19 97.7% 0+0k 0+0io 0pf+0w