Tue Oct 11 03:58:02 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 03:58:02 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6328551 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): -11.98600 37.02700 ymin,ymax (A): -25.92900 22.28800 zmin,zma (A): -10.53600 45.71700 x,y,z range (A): 49.01300 48.21700 56.25300 scale (grids/A): 0.6328551 object centre (A): 12.52050 -1.820499 17.59050 number of atom coordinates read : 2756 total number of charged atoms : 2604 net assigned charge : 1.176015 assigned positive charge : 418.4579 centred at (gu) : 90.31352 90.31114 91.77371 assigned negative charge : -417.2823 centred at (gu) : 90.10934 90.19318 91.71650 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7265 nv = 96 ne = 84 npr = 56539 no. pairs analyzed = 56539 no. exposed pairs = 3331 no. arc points = 23127 no. surface atoms = 1115 nbur = 1641 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 4050 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3700000 number of dielectric boundary points 3548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2382 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8897 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1901957E-09 1.0390097E-08 midg,1,midg; midg,igrid,midg -1.0348466E-08 1.4075265E-08 1,midg,midg; igrid,midg,midg -1.8906222E-08 2.3241363E-08 gauss-seidel spectral radius is 0.9870755 estimated iterations to convergence 72 setup time was (sec) 0.6400000 now iterating at: 03:58:02 rms-change max change #iterations 0.1462965 19.36755 at 10iterations 1.4505595E-02 2.023102 at 20iterations 1.5570907E-03 0.2068310 at 30iterations 2.0269300E-04 2.8640747E-02 at 40iterations 4.2023607E-05 6.5002441E-03 at 50iterations finished qdiffx linear iterations at : 03:58:06 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 4.2023607E-05 6.5002441E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 03:58:06 4.081u 0.249s 0:04.61 93.7% 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 Tue Oct 11 2011 at 03:58:06 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.898565 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): -11.98600 37.02700 ymin,ymax (A): -25.92900 22.28800 zmin,zma (A): -10.53600 45.71700 x,y,z range (A): 49.01300 48.21700 56.25300 scale (grids/A): 1.898565 object centre (A): 12.52050 -1.820499 17.59050 number of atom coordinates read : 2756 total number of charged atoms : 2604 net assigned charge : 1.176015 assigned positive charge : 418.4579 centred at (gu) : 90.94022 90.93321 95.32050 assigned negative charge : -417.2823 centred at (gu) : 90.32800 90.57941 95.14925 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23127 grid for indexing accessible points = 1.400000 m= 28059 mr = 55458 m= 3942 mr = 20584 m= 207 mr = 2325 m= 5 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 562 time to turn everything in is 0.7000000 number of dielectric boundary points 32600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 20478 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) : 0.6328551 object centre at (A) : 12.52050 -1.820499 17.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4482429E-02 -7.1021554E-04 midg,1,midg; midg,igrid,midg -1.0851515E-02 1.9302715E-02 1,midg,midg; igrid,midg,midg -5.9022754E-03 5.3451117E-02 gauss-seidel spectral radius is 0.9986403 estimated iterations to convergence 215 setup time was (sec) 1.000000 now iterating at: 03:58:07 rms-change max change #iterations 4.400953 208.0700 at 10iterations 2.065107 66.55180 at 20iterations 0.9713961 30.96952 at 30iterations 0.4564123 14.90921 at 40iterations 0.2143682 7.472741 at 50iterations 0.1009693 3.280405 at 60iterations 4.7396753E-02 1.455580 at 70iterations 2.2297977E-02 0.7139320 at 80iterations 1.0499458E-02 0.3090773 at 90iterations 4.9294448E-03 0.1635933 at 100iterations 2.3267099E-03 7.4405670E-02 at 110iterations 1.0960518E-03 3.3612728E-02 at 120iterations finished qdiffx linear iterations at : 03:58:16 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 1.0960518E-03 3.3612728E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 03:58:16 9.446u 0.288s 0:10.22 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 03:58:17 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.847848 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): -11.98600 37.02700 ymin,ymax (A): -25.92900 22.28800 zmin,zma (A): -10.53600 45.71700 x,y,z range (A): 49.01300 48.21700 56.25300 scale (grids/A): 2.847848 object centre (A): 12.52050 -1.820499 17.59050 number of atom coordinates read : 2756 total number of charged atoms : 2604 net assigned charge : 1.176015 assigned positive charge : 418.4579 centred at (gu) : 91.41009 91.39962 97.98067 assigned negative charge : -417.2823 centred at (gu) : 90.49184 90.86899 97.72375 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 182209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23127 grid for indexing accessible points = 1.400000 m= 91959 mr = 134239 m= 31687 mr = 75418 m= 7098 mr = 25160 m= 871 mr = 5110 m= 38 mr = 530 m= 0 mr = 7 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 1921 time to turn everything in is 1.790000 number of dielectric boundary points 73398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 20827 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) : 1.898565 object centre at (A) : 12.52050 -1.820499 17.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7255513 0.2353825 midg,1,midg; midg,igrid,midg -0.1453513 0.2644154 1,midg,midg; igrid,midg,midg -4.4977076E-02 0.4947008 gauss-seidel spectral radius is 0.9992597 estimated iterations to convergence 290 setup time was (sec) 2.110000 now iterating at: 03:58:19 rms-change max change #iterations 10.34363 357.4442 at 10iterations 6.045514 146.2946 at 20iterations 3.524125 73.45726 at 30iterations 2.042910 42.32687 at 40iterations 1.186347 24.46766 at 50iterations 0.6849029 12.49618 at 60iterations 0.3949779 8.086262 at 70iterations 0.2284095 3.971654 at 80iterations 0.1319478 2.425975 at 90iterations 7.6226890E-02 1.464943 at 100iterations 4.3829300E-02 0.7992592 at 110iterations 2.5285270E-02 0.5533218 at 120iterations 1.4611299E-02 0.2603569 at 130iterations 8.4509403E-03 0.1438599 at 140iterations 4.8951353E-03 8.5248947E-02 at 150iterations 2.8586253E-03 5.2825928E-02 at 160iterations 1.6818226E-03 3.5595894E-02 at 170iterations 1.0039716E-03 2.0280838E-02 at 180iterations finished qdiffx linear iterations at : 03:58:33 total time elapsed so far: 15.73000 # loops : 180 mean,max change (kT/e) : 1.0039716E-03 2.0280838E-02 energy calculations done at 15.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 03:58:33 15.914u 0.305s 0:16.51 98.1% 0+0k 0+0io 0pf+0w