Mon Oct 10 14:09:07 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 Mon Oct 10 2011 at 14:09:07 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 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: 0.5912837 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): 81.09000 141.2980 ymin,ymax (A): 43.36500 97.64799 zmin,zma (A): -26.80500 27.90900 x,y,z range (A): 60.20798 54.28300 54.71400 scale (grids/A): 0.5912837 object centre (A): 111.1940 70.50650 0.5520000 number of atom coordinates read : 2741 total number of charged atoms : 2551 net assigned charge : 5.500011 assigned positive charge : 408.3667 centred at (gu) : 89.39296 88.60358 90.96255 assigned negative charge : -402.8674 centred at (gu) : 89.43874 88.55615 90.94577 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6432 nv = 96 ne = 84 npr = 54332 no. pairs analyzed = 54332 no. exposed pairs = 3673 no. arc points = 26185 no. surface atoms = 1220 nbur = 1521 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 305 mr = 3265 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0434273E-09 2.7969684E-09 midg,1,midg; midg,igrid,midg 5.1486909E-10 2.2779794E-09 1,midg,midg; igrid,midg,midg 3.5328132E-09 3.9920101E-10 gauss-seidel spectral radius is 0.9852168 estimated iterations to convergence 67 setup time was (sec) 0.5800000 now iterating at: 14:09:08 rms-change max change #iterations 0.1031514 13.46535 at 10iterations 8.4586954E-03 1.289673 at 20iterations 8.0979284E-04 0.1339493 at 30iterations 1.6067513E-04 2.8939247E-02 at 40iterations 5.4757518E-05 1.0578632E-02 at 50iterations finished qdiffx linear iterations at : 14:09:11 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 5.4757518E-05 1.0578632E-02 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 14:09:12 4.490u 0.405s 0:05.33 91.7% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 14:09:12 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 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: 1.773851 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): 81.09000 141.2980 ymin,ymax (A): 43.36500 97.64799 zmin,zma (A): -26.80500 27.90900 x,y,z range (A): 60.20798 54.28300 54.71400 scale (grids/A): 1.773851 object centre (A): 111.1940 70.50650 0.5520000 number of atom coordinates read : 2741 total number of charged atoms : 2551 net assigned charge : 5.500011 assigned positive charge : 408.3667 centred at (gu) : 88.17809 85.81006 92.88702 assigned negative charge : -402.8674 centred at (gu) : 88.31617 85.66831 92.83712 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26185 grid for indexing accessible points = 1.400000 m= 22896 mr = 47242 m= 3070 mr = 15502 m= 168 mr = 1585 m= 4 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 31918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19867 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) : 0.5912837 object centre at (A) : 111.1940 70.50650 0.5520000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6350889E-04 1.1252120E-02 midg,1,midg; midg,igrid,midg 6.4574117E-03 9.8115383E-03 1,midg,midg; igrid,midg,midg 2.7883782E-03 1.5471920E-03 gauss-seidel spectral radius is 0.9984474 estimated iterations to convergence 201 setup time was (sec) 0.8800000 now iterating at: 14:09:13 rms-change max change #iterations 3.752811 159.3299 at 10iterations 1.676789 70.53685 at 20iterations 0.7419367 28.14763 at 30iterations 0.3317352 11.90859 at 40iterations 0.1474503 4.546160 at 50iterations 6.5801114E-02 2.088346 at 60iterations 2.9455500E-02 1.200220 at 70iterations 1.3092100E-02 0.4723930 at 80iterations 5.8640237E-03 0.2092438 at 90iterations 2.6551106E-03 9.6063614E-02 at 100iterations 1.2232458E-03 4.8719406E-02 at 110iterations 5.8690872E-04 2.1299362E-02 at 120iterations finished qdiffx linear iterations at : 14:09:23 total time elapsed so far: 10.27000 # loops : 120 mean,max change (kT/e) : 5.8690872E-04 2.1299362E-02 energy calculations done at 10.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.43000 DelPhi exited at 14:09:23 10.435u 0.447s 0:11.29 96.2% 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 Mon Oct 10 2011 at 14:09:23 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 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: 2.660777 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): 81.09000 141.2980 ymin,ymax (A): 43.36500 97.64799 zmin,zma (A): -26.80500 27.90900 x,y,z range (A): 60.20798 54.28300 54.71400 scale (grids/A): 2.660777 object centre (A): 111.1940 70.50650 0.5520000 number of atom coordinates read : 2741 total number of charged atoms : 2551 net assigned charge : 5.500011 assigned positive charge : 408.3667 centred at (gu) : 87.26695 83.71490 94.33040 assigned negative charge : -402.8674 centred at (gu) : 87.47418 83.50250 94.25550 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 162530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26185 grid for indexing accessible points = 1.400000 m= 76877 mr = 115316 m= 24450 mr = 60487 m= 5240 mr = 18161 m= 661 mr = 3435 m= 35 mr = 347 m= 0 mr = 4 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 72043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 20398 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) : 1.773851 object centre at (A) : 111.1940 70.50650 0.5520000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2622771E-02 0.1482914 midg,1,midg; midg,igrid,midg 0.1388495 0.1216883 1,midg,midg; igrid,midg,midg -0.1357953 5.6299787E-02 gauss-seidel spectral radius is 0.9992131 estimated iterations to convergence 281 setup time was (sec) 1.810000 now iterating at: 14:09:26 rms-change max change #iterations 9.326132 289.0620 at 10iterations 5.445542 129.5511 at 20iterations 3.148765 87.14366 at 30iterations 1.810983 44.57877 at 40iterations 1.041870 25.26608 at 50iterations 0.5940803 13.07373 at 60iterations 0.3389994 7.655998 at 70iterations 0.1924385 4.275497 at 80iterations 0.1097887 2.463711 at 90iterations 6.2262841E-02 1.265245 at 100iterations 3.5257731E-02 0.7390280 at 110iterations 2.0027881E-02 0.4109344 at 120iterations 1.1336487E-02 0.2278748 at 130iterations 6.4301440E-03 0.1348454 at 140iterations 3.6545708E-03 7.6004028E-02 at 150iterations 2.0826093E-03 4.0336609E-02 at 160iterations 1.1957739E-03 2.3983806E-02 at 170iterations 6.9430907E-04 1.5498161E-02 at 180iterations finished qdiffx linear iterations at : 14:09:43 total time elapsed so far: 18.99000 # loops : 180 mean,max change (kT/e) : 6.9430907E-04 1.5498161E-02 energy calculations done at 18.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.16000 DelPhi exited at 14:09:44 19.160u 0.466s 0:20.07 97.7% 0+0k 0+0io 0pf+0w