Tue Oct 11 06:34:12 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+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 06:34:12 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7012706 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): -20.22200 24.48100 ymin,ymax (A): -26.68700 10.64900 zmin,zma (A): -14.12000 36.64500 x,y,z range (A): 44.70300 37.33600 50.76500 scale (grids/A): 0.7012706 object centre (A): 2.129500 -8.019001 11.26250 number of atom coordinates read : 2033 total number of charged atoms : 1922 net assigned charge : 6.945010 assigned positive charge : 312.9711 centred at (gu) : 89.75085 90.87201 89.34885 assigned negative charge : -306.0261 centred at (gu) : 89.56478 90.85395 89.33900 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6787 nv = 96 ne = 84 npr = 40500 no. pairs analyzed = 40500 no. exposed pairs = 2465 no. arc points = 17124 no. surface atoms = 840 nbur = 1193 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 3864 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1538 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7579 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2741338E-08 4.8561418E-08 midg,1,midg; midg,igrid,midg 3.6684213E-08 6.9037775E-08 1,midg,midg; igrid,midg,midg -3.0839658E-08 1.2171836E-07 gauss-seidel spectral radius is 0.9893975 estimated iterations to convergence 79 setup time was (sec) 0.6600000 now iterating at: 06:34:13 rms-change max change #iterations 0.1893623 27.22864 at 10iterations 2.3689434E-02 3.311762 at 20iterations 3.0378394E-03 0.3945370 at 30iterations 4.5997780E-04 7.2582245E-02 at 40iterations 9.4595758E-05 1.3064384E-02 at 50iterations finished qdiffx linear iterations at : 06:34:17 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 9.4595758E-05 1.3064384E-02 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 06:34:18 4.635u 0.454s 0:05.75 88.3% 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 06:34:18 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.103812 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): -20.22200 24.48100 ymin,ymax (A): -26.68700 10.64900 zmin,zma (A): -14.12000 36.64500 x,y,z range (A): 44.70300 37.33600 50.76500 scale (grids/A): 2.103812 object centre (A): 2.129500 -8.019001 11.26250 number of atom coordinates read : 2033 total number of charged atoms : 1922 net assigned charge : 6.945010 assigned positive charge : 312.9711 centred at (gu) : 89.25247 92.61594 88.04662 assigned negative charge : -306.0261 centred at (gu) : 88.69449 92.56205 88.01707 start vw surface at 0.1400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 71909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17124 grid for indexing accessible points = 1.400000 m= 28446 mr = 50973 m= 5480 mr = 21366 m= 475 mr = 3630 m= 9 mr = 236 m= 0 mr = 2 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 30112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 15267 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) : 0.7012706 object centre at (A) : 2.129500 -8.019001 11.26250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6095166E-02 3.1309754E-02 midg,1,midg; midg,igrid,midg 5.3703231E-03 3.2997403E-02 1,midg,midg; igrid,midg,midg 3.2086421E-03 3.5312217E-02 gauss-seidel spectral radius is 0.9988084 estimated iterations to convergence 229 setup time was (sec) 1.100000 now iterating at: 06:34:20 rms-change max change #iterations 4.448450 241.5153 at 10iterations 2.189559 78.66667 at 20iterations 1.078395 35.06662 at 30iterations 0.5334366 16.97174 at 40iterations 0.2623962 8.929167 at 50iterations 0.1299588 4.078701 at 60iterations 6.4169660E-02 2.028751 at 70iterations 3.1850141E-02 1.079726 at 80iterations 1.5768833E-02 0.4786028 at 90iterations 7.8453049E-03 0.2612190 at 100iterations 3.9160978E-03 0.1412048 at 110iterations 1.9846447E-03 6.3060760E-02 at 120iterations finished qdiffx linear iterations at : 06:34:29 total time elapsed so far: 10.25000 # loops : 120 mean,max change (kT/e) : 1.9846447E-03 6.3060760E-02 energy calculations done at 10.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.48000 DelPhi exited at 06:34:30 10.481u 0.449s 0:11.48 95.1% 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 06:34:30 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2033 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.155718 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): -20.22200 24.48100 ymin,ymax (A): -26.68700 10.64900 zmin,zma (A): -14.12000 36.64500 x,y,z range (A): 44.70300 37.33600 50.76500 scale (grids/A): 3.155718 object centre (A): 2.129500 -8.019001 11.26250 number of atom coordinates read : 2033 total number of charged atoms : 1922 net assigned charge : 6.945010 assigned positive charge : 312.9711 centred at (gu) : 88.87865 93.92403 87.07005 assigned negative charge : -306.0261 centred at (gu) : 88.04173 93.84311 87.02559 start vw surface at 0.1400000 fill in re-entrant regions at 0.9400000 boundary points on vw surface= 165960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17124 grid for indexing accessible points = 1.400000 m= 89155 mr = 122759 m= 35814 mr = 74097 m= 10466 mr = 29186 m= 1981 mr = 8096 m= 167 mr = 1415 m= 4 mr = 97 m= 0 mr = 2 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.370000 number of dielectric boundary points 67895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 15376 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) : 2.103812 object centre at (A) : 2.129500 -8.019001 11.26250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6293833 0.2912993 midg,1,midg; midg,igrid,midg 2.8236134E-02 0.2667634 1,midg,midg; igrid,midg,midg 0.1275716 0.2762101 gauss-seidel spectral radius is 0.9992898 estimated iterations to convergence 296 setup time was (sec) 2.740000 now iterating at: 06:34:33 rms-change max change #iterations 10.08427 366.8980 at 10iterations 5.941006 128.4365 at 20iterations 3.499152 90.62076 at 30iterations 2.056231 45.54259 at 40iterations 1.210283 24.33054 at 50iterations 0.7104273 14.07265 at 60iterations 0.4147174 8.457804 at 70iterations 0.2423488 4.813267 at 80iterations 0.1418353 2.533155 at 90iterations 8.3007388E-02 1.611073 at 100iterations 4.8640918E-02 0.9955292 at 110iterations 2.8620083E-02 0.6216965 at 120iterations 1.6924785E-02 0.3099899 at 130iterations 1.0087353E-02 0.1876831 at 140iterations 6.1592329E-03 0.1162186 at 150iterations 3.8585975E-03 7.4676514E-02 at 160iterations 2.5307545E-03 4.5501709E-02 at 170iterations 1.7468394E-03 3.4027100E-02 at 180iterations finished qdiffx linear iterations at : 06:34:49 total time elapsed so far: 18.67000 # loops : 180 mean,max change (kT/e) : 1.7468394E-03 3.4027100E-02 energy calculations done at 18.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.89000 DelPhi exited at 06:34:49 18.897u 0.506s 0:19.69 98.4% 0+0k 0+0io 0pf+0w