Sat Oct 15 13:18:36 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 Sat Oct 15 2011 at 13:18:36 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 = 2561 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6496350 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): -6.372000 43.70800 ymin,ymax (A): 13.08300 67.88300 zmin,zma (A): -11.69600 41.46600 x,y,z range (A): 50.08000 54.80000 53.16200 scale (grids/A): 0.6496350 object centre (A): 18.66800 40.48300 14.88500 number of atom coordinates read : 2561 total number of charged atoms : 2419 net assigned charge : 7.000012 assigned positive charge : 386.2379 centred at (gu) : 89.32360 90.60210 90.10300 assigned negative charge : -379.2386 centred at (gu) : 89.41369 90.74591 90.08740 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7173 nv = 96 ne = 84 npr = 51462 no. pairs analyzed = 51462 no. exposed pairs = 3070 no. arc points = 22053 no. surface atoms = 1051 nbur = 1510 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3898 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2274 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0908122E-08 1.6077829E-08 midg,1,midg; midg,igrid,midg 3.0261276E-08 -9.3516173E-09 1,midg,midg; igrid,midg,midg 3.0676045E-08 1.0917860E-10 gauss-seidel spectral radius is 0.9877188 estimated iterations to convergence 74 setup time was (sec) 0.5800000 now iterating at: 13:18:37 rms-change max change #iterations 0.1505875 20.64791 at 10iterations 1.5387669E-02 2.361684 at 20iterations 1.5788763E-03 0.2382507 at 30iterations 1.6388005E-04 2.3935318E-02 at 40iterations 1.7142907E-05 2.7656555E-03 at 50iterations finished qdiffx linear iterations at : 13:18:40 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.7142907E-05 2.7656555E-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) 4.070000 DelPhi exited at 13:18:41 4.075u 0.431s 0:04.83 93.1% 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 Sat Oct 15 2011 at 13:18:41 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 = 2561 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.948905 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): -6.372000 43.70800 ymin,ymax (A): 13.08300 67.88300 zmin,zma (A): -11.69600 41.46600 x,y,z range (A): 50.08000 54.80000 53.16200 scale (grids/A): 1.948905 object centre (A): 18.66800 40.48300 14.88500 number of atom coordinates read : 2561 total number of charged atoms : 2419 net assigned charge : 7.000012 assigned positive charge : 386.2379 centred at (gu) : 87.97035 91.80567 90.30847 assigned negative charge : -379.2386 centred at (gu) : 88.24078 92.23776 90.26199 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77668 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22053 grid for indexing accessible points = 1.400000 m= 27316 mr = 53597 m= 4470 mr = 20129 m= 345 mr = 2795 m= 2 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1238 time to turn everything in is 0.6300000 number of dielectric boundary points 33121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19077 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) : 0.6496350 object centre at (A) : 18.66800 40.48300 14.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3773402E-02 -3.7486877E-03 midg,1,midg; midg,igrid,midg 4.1685510E-02 2.4131007E-02 1,midg,midg; igrid,midg,midg 1.6235575E-02 -1.3100971E-02 gauss-seidel spectral radius is 0.9986850 estimated iterations to convergence 218 setup time was (sec) 0.9300000 now iterating at: 13:18:42 rms-change max change #iterations 4.364756 225.5261 at 10iterations 2.069227 68.09297 at 20iterations 0.9828281 31.71477 at 30iterations 0.4666265 14.99544 at 40iterations 0.2204527 6.880863 at 50iterations 0.1043991 3.023181 at 60iterations 4.9660947E-02 1.470526 at 70iterations 2.3515437E-02 0.7125549 at 80iterations 1.1197631E-02 0.3607063 at 90iterations 5.3126188E-03 0.1559753 at 100iterations 2.5295301E-03 8.1629872E-02 at 110iterations 1.2000580E-03 3.7105560E-02 at 120iterations finished qdiffx linear iterations at : 13:18:52 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 1.2000580E-03 3.7105560E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 13:18:53 9.539u 0.469s 0:12.42 80.4% 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 Sat Oct 15 2011 at 13:18:53 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 = 2561 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.923357 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): -6.372000 43.70800 ymin,ymax (A): 13.08300 67.88300 zmin,zma (A): -11.69600 41.46600 x,y,z range (A): 50.08000 54.80000 53.16200 scale (grids/A): 2.923357 object centre (A): 18.66800 40.48300 14.88500 number of atom coordinates read : 2561 total number of charged atoms : 2419 net assigned charge : 7.000012 assigned positive charge : 386.2379 centred at (gu) : 86.95528 92.70857 90.46251 assigned negative charge : -379.2386 centred at (gu) : 87.36108 93.35645 90.39295 start vw surface at 0.1300000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 179461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22053 grid for indexing accessible points = 1.400000 m= 89231 mr = 129822 m= 31902 mr = 73095 m= 8083 mr = 25440 m= 1451 mr = 6052 m= 138 mr = 1050 m= 1 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 4582 time to turn everything in is 1.620000 number of dielectric boundary points 74720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 19352 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) : 1.948905 object centre at (A) : 18.66800 40.48300 14.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2348598 -0.2610241 midg,1,midg; midg,igrid,midg 0.5002137 0.1927919 1,midg,midg; igrid,midg,midg 0.2232274 -0.2624597 gauss-seidel spectral radius is 0.9992722 estimated iterations to convergence 293 setup time was (sec) 1.970000 now iterating at: 13:18:56 rms-change max change #iterations 10.10327 406.6985 at 10iterations 5.888497 147.5345 at 20iterations 3.422620 68.15639 at 30iterations 1.987759 42.11298 at 40iterations 1.149826 22.45108 at 50iterations 0.6655493 11.70083 at 60iterations 0.3843825 7.340523 at 70iterations 0.2220026 3.834105 at 80iterations 0.1277696 2.226669 at 90iterations 7.3912024E-02 1.316295 at 100iterations 4.2615566E-02 0.7399650 at 110iterations 2.4556356E-02 0.4586554 at 120iterations 1.4166474E-02 0.2457190 at 130iterations 8.1710257E-03 0.1359148 at 140iterations 4.7232597E-03 8.2406998E-02 at 150iterations 2.7190663E-03 4.6463013E-02 at 160iterations 1.5701076E-03 2.7270794E-02 at 170iterations 9.0510689E-04 1.5220642E-02 at 180iterations finished qdiffx linear iterations at : 13:19:18 total time elapsed so far: 19.29000 # loops : 180 mean,max change (kT/e) : 9.0510689E-04 1.5220642E-02 energy calculations done at 19.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.47000 DelPhi exited at 13:19:18 19.473u 0.491s 0:25.19 79.2% 0+0k 0+0io 0pf+0w