Sat Oct 8 20:19:13 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 Sat Oct 8 2011 at 20:19:13 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN8 803 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6180233 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): -31.32900 17.63800 ymin,ymax (A): -23.63600 22.96100 zmin,zma (A): -12.51000 45.09300 x,y,z range (A): 48.96700 46.59700 57.60300 scale (grids/A): 0.6180233 object centre (A): -6.845500 -0.3374996 16.29150 number of atom coordinates read : 2613 total number of charged atoms : 2474 net assigned charge : 4.500007 assigned positive charge : 396.1650 centred at (gu) : 88.56664 89.19042 89.54745 assigned negative charge : -391.6655 centred at (gu) : 88.45156 89.25800 89.42258 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6446 nv = 96 ne = 84 npr = 54739 no. pairs analyzed = 54739 no. exposed pairs = 3029 no. arc points = 21670 no. surface atoms = 1017 nbur = 1596 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3583 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2000000 number of dielectric boundary points 3143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9655293E-09 1.0226505E-08 midg,1,midg; midg,igrid,midg 9.2841912E-09 -6.1350985E-10 1,midg,midg; igrid,midg,midg -5.3869691E-09 7.8127611E-09 gauss-seidel spectral radius is 0.9864389 estimated iterations to convergence 70 setup time was (sec) 0.3800000 now iterating at: 20:19:14 rms-change max change #iterations 0.1260295 19.61765 at 10iterations 1.1516716E-02 1.596514 at 20iterations 1.0646690E-03 0.1474209 at 30iterations 1.0028953E-04 1.5199661E-02 at 40iterations 9.6625599E-06 1.5792847E-03 at 50iterations finished qdiffx linear iterations at : 20:19:17 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 9.6625599E-06 1.5792847E-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) 3.450000 DelPhi exited at 20:19:17 3.455u 0.196s 0:03.92 92.8% 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 Sat Oct 8 2011 at 20:19:17 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN8 803 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.854070 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): -31.32900 17.63800 ymin,ymax (A): -23.63600 22.96100 zmin,zma (A): -12.51000 45.09300 x,y,z range (A): 48.96700 46.59700 57.60300 scale (grids/A): 1.854070 object centre (A): -6.845500 -0.3374996 16.29150 number of atom coordinates read : 2613 total number of charged atoms : 2474 net assigned charge : 4.500007 assigned positive charge : 396.1650 centred at (gu) : 85.69936 87.57092 88.64189 assigned negative charge : -391.6655 centred at (gu) : 85.35444 87.77370 88.26767 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21670 grid for indexing accessible points = 1.400000 m= 24124 mr = 49076 m= 3345 mr = 17722 m= 157 mr = 2029 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3934 time to turn everything in is 0.3400000 number of dielectric boundary points 29006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19410 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) : 0.6180233 object centre at (A) : -6.845500 -0.3374996 16.29150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1104259E-02 3.1964514E-02 midg,1,midg; midg,igrid,midg 1.3827789E-02 1.3535129E-03 1,midg,midg; igrid,midg,midg -4.0633404E-03 3.5488084E-02 gauss-seidel spectral radius is 0.9985580 estimated iterations to convergence 209 setup time was (sec) 0.5700000 now iterating at: 20:19:18 rms-change max change #iterations 4.011255 146.0156 at 10iterations 1.844410 66.09585 at 20iterations 0.8427812 28.39865 at 30iterations 0.3871866 12.62174 at 40iterations 0.1778726 6.002572 at 50iterations 8.1435733E-02 2.628586 at 60iterations 3.7405934E-02 1.241678 at 70iterations 1.7106308E-02 0.5912321 at 80iterations 7.8662038E-03 0.2567043 at 90iterations 3.6110433E-03 0.1143756 at 100iterations 1.6594735E-03 5.7254314E-02 at 110iterations 7.6024234E-04 2.3719788E-02 at 120iterations finished qdiffx linear iterations at : 20:19:25 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 7.6024234E-04 2.3719788E-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) 7.970000 DelPhi exited at 20:19:26 7.975u 0.202s 0:08.46 96.5% 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 20:19:26 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN8 803 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.781105 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): -31.32900 17.63800 ymin,ymax (A): -23.63600 22.96100 zmin,zma (A): -12.51000 45.09300 x,y,z range (A): 48.96700 46.59700 57.60300 scale (grids/A): 2.781105 object centre (A): -6.845500 -0.3374996 16.29150 number of atom coordinates read : 2613 total number of charged atoms : 2474 net assigned charge : 4.500007 assigned positive charge : 396.1650 centred at (gu) : 83.54893 86.35636 87.96281 assigned negative charge : -391.6655 centred at (gu) : 83.03162 86.66046 87.40150 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 162761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21670 grid for indexing accessible points = 1.400000 m= 79976 mr = 118829 m= 26801 mr = 65496 m= 5889 mr = 21610 m= 693 mr = 4378 m= 23 mr = 449 m= 0 mr = 5 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 12437 time to turn everything in is 0.8800000 number of dielectric boundary points 65376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19791 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) : 1.854070 object centre at (A) : -6.845500 -0.3374996 16.29150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1784580 0.4272835 midg,1,midg; midg,igrid,midg 0.1663190 9.0371491E-03 1,midg,midg; igrid,midg,midg -3.0377543E-02 0.4548525 gauss-seidel spectral radius is 0.9992311 estimated iterations to convergence 285 setup time was (sec) 1.120000 now iterating at: 20:19:27 rms-change max change #iterations 9.485421 330.0878 at 10iterations 5.461618 193.1556 at 20iterations 3.119216 62.72923 at 30iterations 1.782754 38.38418 at 40iterations 1.013690 19.62337 at 50iterations 0.5772622 11.30717 at 60iterations 0.3286556 6.234291 at 70iterations 0.1867982 4.493231 at 80iterations 0.1061746 2.155822 at 90iterations 6.0500816E-02 1.248125 at 100iterations 3.4456015E-02 0.7478313 at 110iterations 1.9552117E-02 0.3445129 at 120iterations 1.1114427E-02 0.2011938 at 130iterations 6.3283020E-03 0.1183987 at 140iterations 3.5954907E-03 7.1731567E-02 at 150iterations 2.0464594E-03 3.5680771E-02 at 160iterations 1.1658951E-03 2.1524429E-02 at 170iterations 6.6696969E-04 1.3622284E-02 at 180iterations finished qdiffx linear iterations at : 20:19:39 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 6.6696969E-04 1.3622284E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 20:19:39 12.867u 0.214s 0:13.35 97.9% 0+0k 0+0io 0pf+0w