Mon Oct 10 16:12:20 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 Mon Oct 10 2011 at 16:12:20 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 = 3845 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: 0.5557811 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): 7.494000 56.61300 ymin,ymax (A): 52.91500 116.9690 zmin,zma (A): -35.65800 26.11800 x,y,z range (A): 49.11900 64.05400 61.77600 scale (grids/A): 0.5557811 object centre (A): 32.05350 84.94200 -4.770000 number of atom coordinates read : 3845 total number of charged atoms : 3755 net assigned charge : 6.500011 assigned positive charge : 572.7082 centred at (gu) : 89.64578 90.40955 91.86756 assigned negative charge : -566.2111 centred at (gu) : 89.60252 90.49797 91.85747 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7961 nv = 96 ne = 84 npr = 76040 no. pairs analyzed = 76040 no. exposed pairs = 4915 no. arc points = 34242 no. surface atoms = 1643 nbur = 2202 mkacc time = 0.2200000 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 = 1.512000 m= 348 mr = 4297 m= 0 mr = 12 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3512 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 10413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0571026E-10 1.1198826E-09 midg,1,midg; midg,igrid,midg 1.4928203E-09 -5.4286015E-10 1,midg,midg; igrid,midg,midg 7.0533260E-11 1.0212385E-09 gauss-seidel spectral radius is 0.9833758 estimated iterations to convergence 64 setup time was (sec) 0.7900000 now iterating at: 16:12:21 rms-change max change #iterations 9.1468260E-02 13.52891 at 10iterations 6.5431050E-03 1.032431 at 20iterations 6.8123057E-04 0.1123371 at 30iterations 1.8224081E-04 2.8373718E-02 at 40iterations 6.7253088E-05 9.3536377E-03 at 50iterations finished qdiffx linear iterations at : 16:12:24 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 6.7253088E-05 9.3536377E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 16:12:25 4.377u 0.191s 0:04.83 94.4% 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 Mon Oct 10 2011 at 16:12:25 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 = 3845 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: 1.667343 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): 7.494000 56.61300 ymin,ymax (A): 52.91500 116.9690 zmin,zma (A): -35.65800 26.11800 x,y,z range (A): 49.11900 64.05400 61.77600 scale (grids/A): 1.667343 object centre (A): 32.05350 84.94200 -4.770000 number of atom coordinates read : 3845 total number of charged atoms : 3755 net assigned charge : 6.500011 assigned positive charge : 572.7082 centred at (gu) : 88.93642 91.22750 95.60142 assigned negative charge : -566.2111 centred at (gu) : 88.80736 91.49349 95.57216 start vw surface at 0.2300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 88690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34242 grid for indexing accessible points = 1.400000 m= 29217 mr = 61880 m= 3460 mr = 20475 m= 103 mr = 1861 m= 0 mr = 15 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 546 time to turn everything in is 0.8000000 number of dielectric boundary points 37239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 361 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 28969 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) : 0.5557811 object centre at (A) : 32.05350 84.94200 -4.770000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7554908E-03 3.7953448E-02 midg,1,midg; midg,igrid,midg 1.9260110E-02 1.4569001E-02 1,midg,midg; igrid,midg,midg 8.0762844E-04 -6.1780582E-03 gauss-seidel spectral radius is 0.9983609 estimated iterations to convergence 196 setup time was (sec) 1.170000 now iterating at: 16:12:26 rms-change max change #iterations 3.982826 158.9715 at 10iterations 1.744578 56.45853 at 20iterations 0.7581743 23.90221 at 30iterations 0.3306422 10.37558 at 40iterations 0.1447310 5.027565 at 50iterations 6.3252486E-02 2.103975 at 60iterations 2.7564347E-02 0.8695679 at 70iterations 1.2099138E-02 0.4555006 at 80iterations 5.3010732E-03 0.1575089 at 90iterations 2.3570457E-03 7.7728271E-02 at 100iterations 1.0736332E-03 3.4842491E-02 at 110iterations 5.1447813E-04 1.6239166E-02 at 120iterations finished qdiffx linear iterations at : 16:12:34 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 5.1447813E-04 1.6239166E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.770000 DelPhi exited at 16:12:35 9.775u 0.218s 0:10.26 97.2% 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 Mon Oct 10 2011 at 16:12:35 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 = 3845 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: 2.501015 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): 7.494000 56.61300 ymin,ymax (A): 52.91500 116.9690 zmin,zma (A): -35.65800 26.11800 x,y,z range (A): 49.11900 64.05400 61.77600 scale (grids/A): 2.501015 object centre (A): 32.05350 84.94200 -4.770000 number of atom coordinates read : 3845 total number of charged atoms : 3755 net assigned charge : 6.500011 assigned positive charge : 572.7082 centred at (gu) : 88.40424 91.84102 98.40166 assigned negative charge : -566.2111 centred at (gu) : 88.21071 92.24020 98.35801 start vw surface at 0.2100000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 206124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34242 grid for indexing accessible points = 1.400000 m= 99778 mr = 151606 m= 30705 mr = 79523 m= 5712 mr = 23506 m= 469 mr = 4001 m= 9 mr = 231 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 1792 time to turn everything in is 1.950000 number of dielectric boundary points 83930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 30018 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) : 1.667343 object centre at (A) : 32.05350 84.94200 -4.770000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1189876 0.9128326 midg,1,midg; midg,igrid,midg 0.2472715 0.3490699 1,midg,midg; igrid,midg,midg 1.7888190E-02 -0.1151796 gauss-seidel spectral radius is 0.9992196 estimated iterations to convergence 283 setup time was (sec) 2.350000 now iterating at: 16:12:37 rms-change max change #iterations 10.21490 342.3181 at 10iterations 5.963569 156.9981 at 20iterations 3.476716 80.01114 at 30iterations 2.009762 42.89544 at 40iterations 1.160767 24.24372 at 50iterations 0.6678318 12.67774 at 60iterations 0.3835251 7.625732 at 70iterations 0.2192188 4.010117 at 80iterations 0.1252939 2.279909 at 90iterations 7.1607113E-02 1.336238 at 100iterations 4.0785000E-02 0.8182538 at 110iterations 2.3286834E-02 0.4685564 at 120iterations 1.3270367E-02 0.2383919 at 130iterations 7.5649894E-03 0.1332569 at 140iterations 4.3182936E-03 7.8632355E-02 at 150iterations 2.4787404E-03 4.2610168E-02 at 160iterations 1.4328561E-03 2.6736975E-02 at 170iterations 8.4534817E-04 1.5192032E-02 at 180iterations finished qdiffx linear iterations at : 16:12:51 total time elapsed so far: 15.67000 # loops : 180 mean,max change (kT/e) : 8.4534817E-04 1.5192032E-02 energy calculations done at 15.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 16:12:51 15.912u 0.244s 0:16.43 98.2% 0+0k 0+0io 0pf+0w