Tue Nov 22 14:09:29 PST 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 Nov 22 2011 at 14:09:32 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 = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6017172 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): -23.74500 35.41900 ymin,ymax (A): -18.71400 20.12300 zmin,zma (A): -2.820000 38.49800 x,y,z range (A): 59.16400 38.83700 41.31800 scale (grids/A): 0.6017172 object centre (A): 5.837002 0.7045002 17.83900 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 3.000004 assigned positive charge : 285.5140 centred at (gu) : 89.60215 90.30892 90.19194 assigned negative charge : -282.5143 centred at (gu) : 89.61046 90.39532 90.32925 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4699 nv = 96 ne = 84 npr = 40045 no. pairs analyzed = 40045 no. exposed pairs = 2431 no. arc points = 17161 no. surface atoms = 821 nbur = 1125 mkacc time = 7.0000000E-02 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 = 1.456000 m= 209 mr = 2549 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1500000 number of dielectric boundary points 2350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1765 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5819 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9455458E-09 -2.6479829E-09 midg,1,midg; midg,igrid,midg 3.5212357E-09 -1.1503754E-09 1,midg,midg; igrid,midg,midg 1.7599530E-09 1.0515188E-09 gauss-seidel spectral radius is 0.9856493 estimated iterations to convergence 68 setup time was (sec) 0.3700000 now iterating at: 14:09:32 rms-change max change #iterations 9.1845706E-02 18.01296 at 10iterations 7.9186959E-03 1.416008 at 20iterations 6.7068817E-04 0.1464005 at 30iterations 5.6251545E-05 9.1066360E-03 at 40iterations 4.7970157E-06 8.6975098E-04 at 50iterations finished qdiffx linear iterations at : 14:09:39 total time elapsed so far: 3.660000 # loops : 50 mean,max change (kT/e) : 4.7970157E-06 8.6975098E-04 energy calculations done at 3.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 14:09:40 3.798u 0.247s 0:08.40 47.9% 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 Tue Nov 22 2011 at 14:09:41 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 = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.805152 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): -23.74500 35.41900 ymin,ymax (A): -18.71400 20.12300 zmin,zma (A): -2.820000 38.49800 x,y,z range (A): 59.16400 38.83700 41.31800 scale (grids/A): 1.805152 object centre (A): 5.837002 0.7045002 17.83900 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 3.000004 assigned positive charge : 285.5140 centred at (gu) : 88.80653 90.92690 90.57582 assigned negative charge : -282.5143 centred at (gu) : 88.83162 91.18608 90.98788 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 51473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17161 grid for indexing accessible points = 1.400000 m= 17991 mr = 35139 m= 2324 mr = 13375 m= 76 mr = 1398 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1139 time to turn everything in is 0.2500000 number of dielectric boundary points 21945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14205 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) : 0.6017172 object centre at (A) : 5.837002 0.7045002 17.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6072415E-03 -5.7524862E-03 midg,1,midg; midg,igrid,midg 2.1209323E-03 -3.8591661E-03 1,midg,midg; igrid,midg,midg 3.9621394E-02 3.2880895E-02 gauss-seidel spectral radius is 0.9984035 estimated iterations to convergence 199 setup time was (sec) 0.5200000 now iterating at: 14:09:44 rms-change max change #iterations 3.150061 188.5780 at 10iterations 1.384044 58.03698 at 20iterations 0.6119550 23.52015 at 30iterations 0.2683448 10.25066 at 40iterations 0.1180480 4.734967 at 50iterations 5.1685464E-02 2.202326 at 60iterations 2.2815628E-02 0.8300076 at 70iterations 1.0031918E-02 0.4394302 at 80iterations 4.4135996E-03 0.1809196 at 90iterations 1.9408589E-03 7.5000763E-02 at 100iterations 8.5518649E-04 3.1235456E-02 at 110iterations 3.7683605E-04 1.5201569E-02 at 120iterations finished qdiffx linear iterations at : 14:10:00 total time elapsed so far: 8.720000 # loops : 120 mean,max change (kT/e) : 3.7683605E-04 1.5201569E-02 energy calculations done at 8.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.860000 DelPhi exited at 14:10:00 8.859u 0.362s 0:19.43 47.4% 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 Nov 22 2011 at 14:10:01 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 = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.707728 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): -23.74500 35.41900 ymin,ymax (A): -18.71400 20.12300 zmin,zma (A): -2.820000 38.49800 x,y,z range (A): 59.16400 38.83700 41.31800 scale (grids/A): 2.707728 object centre (A): 5.837002 0.7045002 17.83900 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 3.000004 assigned positive charge : 285.5140 centred at (gu) : 88.20975 91.39027 90.86370 assigned negative charge : -282.5143 centred at (gu) : 88.24746 91.77926 91.48186 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 118946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17161 grid for indexing accessible points = 1.400000 m= 59357 mr = 85147 m= 19867 mr = 48760 m= 3930 mr = 16105 m= 302 mr = 2841 m= 12 mr = 137 m= 0 mr = 2 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3833 time to turn everything in is 0.6800000 number of dielectric boundary points 49422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14508 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) : 1.805152 object centre at (A) : 5.837002 0.7045002 17.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7831455E-02 -5.2662168E-02 midg,1,midg; midg,igrid,midg 1.0746128E-02 -3.8158458E-02 1,midg,midg; igrid,midg,midg 0.4496987 0.2956344 gauss-seidel spectral radius is 0.9991767 estimated iterations to convergence 275 setup time was (sec) 0.9600000 now iterating at: 14:10:04 rms-change max change #iterations 7.634246 384.5229 at 10iterations 4.277318 124.5741 at 20iterations 2.392536 53.97694 at 30iterations 1.332887 30.81898 at 40iterations 0.7406460 20.02108 at 50iterations 0.4132657 10.53730 at 60iterations 0.2295002 6.070633 at 70iterations 0.1279285 2.973185 at 80iterations 7.1053267E-02 1.706257 at 90iterations 3.9497465E-02 0.9187813 at 100iterations 2.1968001E-02 0.5171053 at 110iterations 1.2215870E-02 0.2738323 at 120iterations 6.7964057E-03 0.1499557 at 130iterations 3.7769233E-03 8.2711220E-02 at 140iterations 2.0993191E-03 4.4679642E-02 at 150iterations 1.1657848E-03 2.6805282E-02 at 160iterations 6.4756052E-04 1.3729095E-02 at 170iterations 3.6049687E-04 8.1367493E-03 at 180iterations finished qdiffx linear iterations at : 14:10:32 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 3.6049687E-04 8.1367493E-03 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 14:10:32 14.018u 0.347s 0:31.14 46.0% 0+0k 0+0io 0pf+0w