Sun Oct 9 12:02:23 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 Sun Oct 9 2011 at 12:02:23 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 = 2397 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: 0.6819924 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): -6.932000 44.66600 ymin,ymax (A): -13.74200 38.45800 zmin,zma (A): 0.5020000 45.00000 x,y,z range (A): 51.59800 52.20000 44.49800 scale (grids/A): 0.6819924 object centre (A): 18.86700 12.35800 22.75100 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 5.500015 assigned positive charge : 365.9930 centred at (gu) : 89.78648 90.81794 91.23399 assigned negative charge : -360.4936 centred at (gu) : 89.82645 90.92536 91.35223 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7622 nv = 96 ne = 84 npr = 47653 no. pairs analyzed = 47653 no. exposed pairs = 2929 no. arc points = 20838 no. surface atoms = 985 nbur = 1412 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4307 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2034 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8674 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8926243E-08 -1.6230938E-08 midg,1,midg; midg,igrid,midg 5.0320939E-08 -1.0575142E-08 1,midg,midg; igrid,midg,midg 3.9922696E-08 1.2485128E-08 gauss-seidel spectral radius is 0.9888357 estimated iterations to convergence 77 setup time was (sec) 0.3600000 now iterating at: 12:02:24 rms-change max change #iterations 0.1851272 26.52080 at 10iterations 2.1257922E-02 2.904598 at 20iterations 2.4604220E-03 0.3389359 at 30iterations 3.1532798E-04 3.9260864E-02 at 40iterations 4.9664242E-05 6.7472458E-03 at 50iterations finished qdiffx linear iterations at : 12:02:26 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.9664242E-05 6.7472458E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 12:02:27 3.308u 0.175s 0:03.80 91.3% 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 Sun Oct 9 2011 at 12:02:27 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 = 2397 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: 2.045977 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): -6.932000 44.66600 ymin,ymax (A): -13.74200 38.45800 zmin,zma (A): 0.5020000 45.00000 x,y,z range (A): 51.59800 52.20000 44.49800 scale (grids/A): 2.045977 object centre (A): 18.86700 12.35800 22.75100 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 5.500015 assigned positive charge : 365.9930 centred at (gu) : 89.35896 92.45319 93.70145 assigned negative charge : -360.4936 centred at (gu) : 89.47903 92.77575 94.05650 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20838 grid for indexing accessible points = 1.400000 m= 32211 mr = 55978 m= 6326 mr = 24455 m= 545 mr = 4150 m= 19 mr = 248 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 580 time to turn everything in is 0.4000000 number of dielectric boundary points 34698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17837 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) : 0.6819924 object centre at (A) : 18.86700 12.35800 22.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9954520E-02 2.1767349E-03 midg,1,midg; midg,igrid,midg 2.6340384E-02 -2.3670111E-02 1,midg,midg; igrid,midg,midg 4.7779903E-02 -2.3816971E-02 gauss-seidel spectral radius is 0.9987924 estimated iterations to convergence 228 setup time was (sec) 0.6100000 now iterating at: 12:02:28 rms-change max change #iterations 4.680625 240.8571 at 10iterations 2.289778 90.26749 at 20iterations 1.116551 32.95408 at 30iterations 0.5465795 15.57692 at 40iterations 0.2678719 7.910094 at 50iterations 0.1313044 3.869053 at 60iterations 6.4419821E-02 2.086384 at 70iterations 3.1591918E-02 0.9718761 at 80iterations 1.5542728E-02 0.4288530 at 90iterations 7.6289163E-03 0.2515221 at 100iterations 3.7741880E-03 0.1154349 at 110iterations 1.8764548E-03 5.5999756E-02 at 120iterations finished qdiffx linear iterations at : 12:02:35 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.8764548E-03 5.5999756E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 12:02:35 7.723u 0.179s 0:08.17 96.5% 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 Sun Oct 9 2011 at 12:02:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 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: 3.068965 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): -6.932000 44.66600 ymin,ymax (A): -13.74200 38.45800 zmin,zma (A): 0.5020000 45.00000 x,y,z range (A): 51.59800 52.20000 44.49800 scale (grids/A): 3.068965 object centre (A): 18.86700 12.35800 22.75100 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 5.500015 assigned positive charge : 365.9930 centred at (gu) : 89.03822 93.67962 95.55210 assigned negative charge : -360.4936 centred at (gu) : 89.21861 94.16366 96.08470 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 185598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20838 grid for indexing accessible points = 1.400000 m= 99529 mr = 135287 m= 41275 mr = 82383 m= 11827 mr = 34050 m= 2252 mr = 9091 m= 223 mr = 1596 m= 10 mr = 129 m= 0 mr = 4 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1990 time to turn everything in is 1.080000 number of dielectric boundary points 78174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 18048 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) : 2.045977 object centre at (A) : 18.86700 12.35800 22.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5407525 -0.1355724 midg,1,midg; midg,igrid,midg 0.5763580 -0.2360513 1,midg,midg; igrid,midg,midg 0.4881337 -0.4761491 gauss-seidel spectral radius is 0.9992901 estimated iterations to convergence 296 setup time was (sec) 1.310000 now iterating at: 12:02:37 rms-change max change #iterations 10.58551 410.5164 at 10iterations 6.247139 127.1395 at 20iterations 3.673881 95.24121 at 30iterations 2.157264 48.52124 at 40iterations 1.263657 25.39266 at 50iterations 0.7395350 13.65521 at 60iterations 0.4328434 7.389183 at 70iterations 0.2521957 4.178223 at 80iterations 0.1470300 2.518536 at 90iterations 8.5754581E-02 1.453922 at 100iterations 5.0132595E-02 0.9025345 at 110iterations 2.9186631E-02 0.5979307 at 120iterations 1.7105391E-02 0.2977676 at 130iterations 1.0007106E-02 0.1731291 at 140iterations 5.9226849E-03 0.1012688 at 150iterations 3.5287293E-03 6.3758850E-02 at 160iterations 2.1486946E-03 3.8146973E-02 at 170iterations 1.3383009E-03 2.6596069E-02 at 180iterations finished qdiffx linear iterations at : 12:02:48 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.3383009E-03 2.6596069E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 12:02:49 12.888u 0.208s 0:13.44 97.3% 0+0k 0+0io 0pf+0w