Tue Nov 22 14:09:04 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 14:09:04 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 = 1964 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: 0.6431449 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): -6.004000 34.41700 ymin,ymax (A): -3.598000 47.72800 zmin,zma (A): -24.34800 31.00500 x,y,z range (A): 40.42100 51.32600 55.35300 scale (grids/A): 0.6431449 object centre (A): 14.20650 22.06500 3.328501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.80783 92.64507 90.14310 assigned negative charge : -284.8263 centred at (gu) : 90.91714 92.78065 90.08965 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5496 nv = 96 ne = 84 npr = 41204 no. pairs analyzed = 41204 no. exposed pairs = 2403 no. arc points = 16977 no. surface atoms = 814 nbur = 1150 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 264 mr = 3093 m= 0 mr = 35 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.1600000 number of dielectric boundary points 2632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1704 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6532 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4790214E-10 1.0429169E-08 midg,1,midg; midg,igrid,midg 1.0053634E-08 -1.3723289E-08 1,midg,midg; igrid,midg,midg 1.2789777E-08 -6.0217040E-09 gauss-seidel spectral radius is 0.9874155 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 14:09:05 rms-change max change #iterations 0.1256201 20.50031 at 10iterations 1.2569252E-02 2.229736 at 20iterations 1.2269414E-03 0.1999378 at 30iterations 1.2582510E-04 2.0160675E-02 at 40iterations 1.2262116E-05 1.9817352E-03 at 50iterations finished qdiffx linear iterations at : 14:09:08 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.2262116E-05 1.9817352E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 14:09:09 3.638u 0.224s 0:05.14 74.9% 0+0k 0+0io 5pf+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 14:09:09 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 = 1964 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: 1.929435 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): -6.004000 34.41700 ymin,ymax (A): -3.598000 47.72800 zmin,zma (A): -24.34800 31.00500 x,y,z range (A): 40.42100 51.32600 55.35300 scale (grids/A): 1.929435 object centre (A): 14.20650 22.06500 3.328501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.42328 97.93522 90.42928 assigned negative charge : -284.8263 centred at (gu) : 92.75169 98.34197 90.26897 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 21415 mr = 40922 m= 3114 mr = 16209 m= 137 mr = 1955 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1229 time to turn everything in is 0.3100000 number of dielectric boundary points 24457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14415 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) : 0.6431449 object centre at (A) : 14.20650 22.06500 3.328501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4441633E-02 1.4405184E-02 midg,1,midg; midg,igrid,midg 2.9431785E-02 -8.0814250E-03 1,midg,midg; igrid,midg,midg 8.3731497E-03 -4.7711525E-03 gauss-seidel spectral radius is 0.9985881 estimated iterations to convergence 211 setup time was (sec) 0.5400000 now iterating at: 14:09:10 rms-change max change #iterations 3.642359 166.3092 at 10iterations 1.685317 62.64230 at 20iterations 0.7793809 28.71757 at 30iterations 0.3615943 12.71120 at 40iterations 0.1673172 5.525777 at 50iterations 7.6804422E-02 2.728911 at 60iterations 3.5501316E-02 1.233627 at 70iterations 1.6429629E-02 0.5947189 at 80iterations 7.5966753E-03 0.2614992 at 90iterations 3.5264671E-03 0.1189671 at 100iterations 1.6218218E-03 5.6512736E-02 at 110iterations 7.5188797E-04 2.9609680E-02 at 120iterations finished qdiffx linear iterations at : 14:09:18 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 7.5188797E-04 2.9609680E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 14:09:18 8.205u 0.228s 0:08.90 94.6% 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 14:09:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.894152 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): -6.004000 34.41700 ymin,ymax (A): -3.598000 47.72800 zmin,zma (A): -24.34800 31.00500 x,y,z range (A): 40.42100 51.32600 55.35300 scale (grids/A): 2.894152 object centre (A): 14.20650 22.06500 3.328501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 93.63492 101.9027 90.64400 assigned negative charge : -284.8263 centred at (gu) : 94.12764 102.5130 90.40360 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 136197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 69141 mr = 98777 m= 25123 mr = 57290 m= 5536 mr = 20800 m= 688 mr = 4190 m= 42 mr = 443 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 4314 time to turn everything in is 0.7700000 number of dielectric boundary points 55213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14654 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) : 1.929435 object centre at (A) : 14.20650 22.06500 3.328501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.075896 3.8038023E-02 midg,1,midg; midg,igrid,midg 0.3002458 -0.1202210 1,midg,midg; igrid,midg,midg 4.3837842E-02 -2.8235141E-02 gauss-seidel spectral radius is 0.9992304 estimated iterations to convergence 285 setup time was (sec) 1.040000 now iterating at: 14:09:19 rms-change max change #iterations 8.485276 347.4835 at 10iterations 4.856264 112.9908 at 20iterations 2.748767 59.59454 at 30iterations 1.559286 31.57126 at 40iterations 0.8842455 18.18446 at 50iterations 0.5013888 10.04311 at 60iterations 0.2836608 6.219582 at 70iterations 0.1610816 3.625364 at 80iterations 9.1273598E-02 1.833735 at 90iterations 5.1790744E-02 1.134404 at 100iterations 2.9374693E-02 0.6304426 at 110iterations 1.6601404E-02 0.3452911 at 120iterations 9.4366102E-03 0.2004349 at 130iterations 5.3375917E-03 0.1060209 at 140iterations 3.0310852E-03 6.8023205E-02 at 150iterations 1.7195523E-03 3.5850525E-02 at 160iterations 9.7268709E-04 1.8234372E-02 at 170iterations 5.5229740E-04 1.2789726E-02 at 180iterations finished qdiffx linear iterations at : 14:09:32 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 5.5229740E-04 1.2789726E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 14:09:32 13.546u 0.259s 0:14.24 96.8% 0+0k 0+0io 0pf+0w