Sat Oct 8 20:44:16 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 20:44:16 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 457 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6501095 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): -31.77500 17.46900 ymin,ymax (A): -23.14900 23.30000 zmin,zma (A): -12.45600 42.30400 x,y,z range (A): 49.24400 46.44900 54.76000 scale (grids/A): 0.6501095 object centre (A): -7.153000 7.5499535E-02 14.92400 number of atom coordinates read : 2517 total number of charged atoms : 2385 net assigned charge : 2.420009 assigned positive charge : 382.1132 centred at (gu) : 88.59907 89.02313 90.11343 assigned negative charge : -379.6937 centred at (gu) : 88.47777 89.05345 90.04446 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7068 nv = 96 ne = 84 npr = 52267 no. pairs analyzed = 52267 no. exposed pairs = 2898 no. arc points = 20986 no. surface atoms = 980 nbur = 1537 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 4045 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.3800000 number of dielectric boundary points 3375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2010 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8410 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3159659E-09 1.5496948E-08 midg,1,midg; midg,igrid,midg 1.1575848E-08 3.4862951E-10 1,midg,midg; igrid,midg,midg -1.8306247E-08 1.6950784E-08 gauss-seidel spectral radius is 0.9877295 estimated iterations to convergence 74 setup time was (sec) 0.7200000 now iterating at: 20:44:18 rms-change max change #iterations 0.1571158 20.50126 at 10iterations 1.6169580E-02 2.213638 at 20iterations 1.6320879E-03 0.2088928 at 30iterations 1.7181900E-04 2.2785902E-02 at 40iterations 1.7911305E-05 2.8228760E-03 at 50iterations finished qdiffx linear iterations at : 20:44:21 total time elapsed so far: 4.670000 # loops : 50 mean,max change (kT/e) : 1.7911305E-05 2.8228760E-03 energy calculations done at 4.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.880000 DelPhi exited at 20:44:22 4.888u 0.474s 0:05.63 95.0% 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 20:44:22 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 457 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.950329 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): -31.77500 17.46900 ymin,ymax (A): -23.14900 23.30000 zmin,zma (A): -12.45600 42.30400 x,y,z range (A): 49.24400 46.44900 54.76000 scale (grids/A): 1.950329 object centre (A): -7.153000 7.5499535E-02 14.92400 number of atom coordinates read : 2517 total number of charged atoms : 2385 net assigned charge : 2.420009 assigned positive charge : 382.1132 centred at (gu) : 85.79679 87.06882 90.34007 assigned negative charge : -379.6937 centred at (gu) : 85.43324 87.16032 90.13322 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 76505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20986 grid for indexing accessible points = 1.400000 m= 27753 mr = 54066 m= 4447 mr = 20839 m= 249 mr = 2834 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 6528 time to turn everything in is 0.8000000 number of dielectric boundary points 31133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 18781 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) : 0.6501095 object centre at (A) : -7.153000 7.5499535E-02 14.92400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2950483E-02 1.3626658E-03 midg,1,midg; midg,igrid,midg 1.6286181E-02 5.3132320E-04 1,midg,midg; igrid,midg,midg -2.9321206E-03 4.4230018E-02 gauss-seidel spectral radius is 0.9986867 estimated iterations to convergence 219 setup time was (sec) 1.230000 now iterating at: 20:44:24 rms-change max change #iterations 4.386019 173.9821 at 10iterations 2.091036 66.81068 at 20iterations 0.9932028 32.41691 at 30iterations 0.4724045 17.00147 at 40iterations 0.2242245 7.239275 at 50iterations 0.1068480 3.336639 at 60iterations 5.0783839E-02 1.653191 at 70iterations 2.4145937E-02 0.7311096 at 80iterations 1.1481349E-02 0.3523254 at 90iterations 5.4559410E-03 0.1826859 at 100iterations 2.5925585E-03 8.0043793E-02 at 110iterations 1.2385646E-03 3.7422180E-02 at 120iterations finished qdiffx linear iterations at : 20:44:34 total time elapsed so far: 11.90000 # loops : 120 mean,max change (kT/e) : 1.2385646E-03 3.7422180E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 20:44:35 12.126u 0.494s 0:12.90 97.7% 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 Sat Oct 8 2011 at 20:44:35 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 457 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.925493 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): -31.77500 17.46900 ymin,ymax (A): -23.14900 23.30000 zmin,zma (A): -12.45600 42.30400 x,y,z range (A): 49.24400 46.44900 54.76000 scale (grids/A): 2.925493 object centre (A): -7.153000 7.5499535E-02 14.92400 number of atom coordinates read : 2517 total number of charged atoms : 2385 net assigned charge : 2.420009 assigned positive charge : 382.1132 centred at (gu) : 83.69504 85.60319 90.50990 assigned negative charge : -379.6937 centred at (gu) : 83.14983 85.74053 90.19983 start vw surface at 0.1400000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 176772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20986 grid for indexing accessible points = 1.400000 m= 90230 mr = 130441 m= 32747 mr = 74835 m= 7900 mr = 26497 m= 1101 mr = 6063 m= 67 mr = 731 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 22606 time to turn everything in is 2.030000 number of dielectric boundary points 70222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 19080 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) : 1.950329 object centre at (A) : -7.153000 7.5499535E-02 14.92400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1246928 -5.6051458E-03 midg,1,midg; midg,igrid,midg 0.1660140 -5.8147531E-02 1,midg,midg; igrid,midg,midg 3.2826629E-02 0.5122088 gauss-seidel spectral radius is 0.9992654 estimated iterations to convergence 291 setup time was (sec) 2.410000 now iterating at: 20:44:38 rms-change max change #iterations 10.09300 383.8424 at 10iterations 5.849586 131.1636 at 20iterations 3.380457 63.96840 at 30iterations 1.952191 41.88176 at 40iterations 1.130312 19.87254 at 50iterations 0.6519504 13.77574 at 60iterations 0.3751315 8.528875 at 70iterations 0.2166537 4.266834 at 80iterations 0.1244656 2.048569 at 90iterations 7.1796522E-02 1.240116 at 100iterations 4.1422840E-02 0.7691597 at 110iterations 2.3794126E-02 0.4529724 at 120iterations 1.3689946E-02 0.2311382 at 130iterations 7.8916019E-03 0.1468897 at 140iterations 4.5459257E-03 8.3132744E-02 at 150iterations 2.6195322E-03 4.9138546E-02 at 160iterations 1.5131066E-03 2.8209686E-02 at 170iterations 8.7472063E-04 1.5718460E-02 at 180iterations finished qdiffx linear iterations at : 20:44:55 total time elapsed so far: 19.44000 # loops : 180 mean,max change (kT/e) : 8.7472063E-04 1.5718460E-02 energy calculations done at 19.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.66000 DelPhi exited at 20:44:56 19.661u 0.544s 0:20.50 98.5% 0+0k 0+0io 0pf+0w