Wed Dec 21 14:21:27 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+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 Wed Dec 21 2011 at 14:21:28 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1937 !!! WARNING: MET 145 has a net charge of -0.0720 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: 0.6381301 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): -35.08800 11.00700 ymin,ymax (A): 1.270000 40.78600 zmin,zma (A): -0.4540000 55.33400 x,y,z range (A): 46.09500 39.51600 55.78800 scale (grids/A): 0.6381301 object centre (A): -12.04050 21.02800 27.44000 number of atom coordinates read : 1937 total number of charged atoms : 1805 net assigned charge : -7.1993321E-02 assigned positive charge : 286.2031 centred at (gu) : 90.27454 89.53098 90.13070 assigned negative charge : -286.2753 centred at (gu) : 90.17278 89.66419 90.10548 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5415 nv = 96 ne = 84 npr = 40238 no. pairs analyzed = 40238 no. exposed pairs = 2325 no. arc points = 16550 no. surface atoms = 794 nbur = 1143 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 3093 m= 0 mr = 45 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1500000 number of dielectric boundary points 2558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1655 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6343 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1786004E-09 1.9400770E-09 midg,1,midg; midg,igrid,midg 1.1713116E-08 -1.0137061E-08 1,midg,midg; igrid,midg,midg -8.0904066E-09 8.5601322E-09 gauss-seidel spectral radius is 0.9872185 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 14:21:28 rms-change max change #iterations 0.1246554 20.92456 at 10iterations 1.2150104E-02 2.075768 at 20iterations 1.1896446E-03 0.1907787 at 30iterations 1.1668891E-04 2.0242691E-02 at 40iterations 1.1261867E-05 1.8582344E-03 at 50iterations finished qdiffx linear iterations at : 14:21:32 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.1261867E-05 1.8582344E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 14:21:43 3.993u 0.293s 0:16.02 26.7% 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 Wed Dec 21 2011 at 14:21:44 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1937 !!! WARNING: MET 145 has a net charge of -0.0720 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: 1.914390 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): -35.08800 11.00700 ymin,ymax (A): 1.270000 40.78600 zmin,zma (A): -0.4540000 55.33400 x,y,z range (A): 46.09500 39.51600 55.78800 scale (grids/A): 1.914390 object centre (A): -12.04050 21.02800 27.44000 number of atom coordinates read : 1937 total number of charged atoms : 1805 net assigned charge : -7.1993321E-02 assigned positive charge : 286.2031 centred at (gu) : 90.82365 88.59294 90.39215 assigned negative charge : -286.2753 centred at (gu) : 90.51846 88.99277 90.31660 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 57876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16550 grid for indexing accessible points = 1.400000 m= 22013 mr = 40330 m= 3529 mr = 17017 m= 185 mr = 2396 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 899 time to turn everything in is 0.3100000 number of dielectric boundary points 23791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4100000 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) : 0.6381301 object centre at (A) : -12.04050 21.02800 27.44000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6813449E-03 1.2751123E-02 midg,1,midg; midg,igrid,midg 2.0630981E-03 -1.8355975E-02 1,midg,midg; igrid,midg,midg -5.8990936E-03 -2.4726447E-03 gauss-seidel spectral radius is 0.9985709 estimated iterations to convergence 210 setup time was (sec) 0.5700000 now iterating at: 14:21:45 rms-change max change #iterations 3.637545 164.6490 at 10iterations 1.673297 63.71737 at 20iterations 0.7748955 26.46840 at 30iterations 0.3572791 14.40615 at 40iterations 0.1634805 5.756885 at 50iterations 7.5266756E-02 2.725360 at 60iterations 3.4717157E-02 1.398193 at 70iterations 1.5968341E-02 0.6288147 at 80iterations 7.3451102E-03 0.2705517 at 90iterations 3.3839012E-03 0.1263046 at 100iterations 1.5571518E-03 5.2490234E-02 at 110iterations 7.1498309E-04 2.4382591E-02 at 120iterations finished qdiffx linear iterations at : 14:21:55 total time elapsed so far: 10.66000 # loops : 120 mean,max change (kT/e) : 7.1498309E-04 2.4382591E-02 energy calculations done at 10.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 14:22:15 10.801u 0.301s 0:31.49 35.2% 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 Wed Dec 21 2011 at 14:22:17 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1937 !!! WARNING: MET 145 has a net charge of -0.0720 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: 2.871585 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): -35.08800 11.00700 ymin,ymax (A): 1.270000 40.78600 zmin,zma (A): -0.4540000 55.33400 x,y,z range (A): 46.09500 39.51600 55.78800 scale (grids/A): 2.871585 object centre (A): -12.04050 21.02800 27.44000 number of atom coordinates read : 1937 total number of charged atoms : 1805 net assigned charge : -7.1993321E-02 assigned positive charge : 286.2031 centred at (gu) : 91.23534 87.88937 90.58820 assigned negative charge : -286.2753 centred at (gu) : 90.77775 88.48922 90.47498 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 133384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16550 grid for indexing accessible points = 1.400000 m= 70045 mr = 96989 m= 26697 mr = 58761 m= 6422 mr = 22398 m= 841 mr = 5044 m= 41 mr = 607 m= 0 mr = 20 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 3014 time to turn everything in is 0.8500000 number of dielectric boundary points 53611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14440 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) : 1.914390 object centre at (A) : -12.04050 21.02800 27.44000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7460326E-02 5.1758885E-02 midg,1,midg; midg,igrid,midg -7.3081516E-03 -0.2071870 1,midg,midg; igrid,midg,midg -8.2159325E-02 -8.9574784E-02 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 1.210000 now iterating at: 14:22:20 rms-change max change #iterations 8.490658 309.0129 at 10iterations 4.850726 152.7977 at 20iterations 2.753512 62.73973 at 30iterations 1.565439 33.81691 at 40iterations 0.8865010 16.95184 at 50iterations 0.5034298 10.44360 at 60iterations 0.2842264 5.715820 at 70iterations 0.1610107 3.031708 at 80iterations 9.1070242E-02 2.044505 at 90iterations 5.1457819E-02 1.140465 at 100iterations 2.9105784E-02 0.5801988 at 110iterations 1.6462762E-02 0.3488846 at 120iterations 9.3478477E-03 0.1813707 at 130iterations 5.2642971E-03 0.1208720 at 140iterations 2.9859194E-03 6.0683250E-02 at 150iterations 1.6917251E-03 3.1492591E-02 at 160iterations 9.5278467E-04 1.8101692E-02 at 170iterations 5.4071879E-04 1.0824442E-02 at 180iterations finished qdiffx linear iterations at : 14:22:35 total time elapsed so far: 16.42000 # loops : 180 mean,max change (kT/e) : 5.4071879E-04 1.0824442E-02 energy calculations done at 16.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.57000 DelPhi exited at 14:22:48 16.571u 0.371s 0:31.52 53.7% 0+0k 0+0io 0pf+0w