Tue Nov 22 14:10:15 PST 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 Nov 22 2011 at 14:10:17 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6473316 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): -5.079000 35.40400 ymin,ymax (A): -3.943000 48.52600 zmin,zma (A): -24.37700 30.61800 x,y,z range (A): 40.48300 52.46900 54.99500 scale (grids/A): 0.6473316 object centre (A): 15.16250 22.29150 3.120501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 90.42455 92.77235 90.29943 assigned negative charge : -287.6263 centred at (gu) : 90.54285 92.87992 90.22319 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5647 nv = 96 ne = 84 npr = 40434 no. pairs analyzed = 40434 no. exposed pairs = 2376 no. arc points = 17226 no. surface atoms = 814 nbur = 1150 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3178 m= 0 mr = 41 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1600000 number of dielectric boundary points 2741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6600 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1248492E-09 1.4510142E-08 midg,1,midg; midg,igrid,midg 9.4334984E-09 -1.0672432E-08 1,midg,midg; igrid,midg,midg 1.6373908E-08 -7.4481177E-09 gauss-seidel spectral radius is 0.9875787 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 14:10:17 rms-change max change #iterations 0.1317676 20.51269 at 10iterations 1.3133287E-02 2.059324 at 20iterations 1.3420072E-03 0.2049239 at 30iterations 1.3539493E-04 2.1862507E-02 at 40iterations 1.3583040E-05 2.1629333E-03 at 50iterations finished qdiffx linear iterations at : 14:10:23 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 1.3583040E-05 2.1629333E-03 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 14:10:24 3.738u 0.232s 0:07.56 52.3% 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 Tue Nov 22 2011 at 14:10:25 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.941995 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): -5.079000 35.40400 ymin,ymax (A): -3.943000 48.52600 zmin,zma (A): -24.37700 30.61800 x,y,z range (A): 40.48300 52.46900 54.99500 scale (grids/A): 1.941995 object centre (A): 15.16250 22.29150 3.120501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 91.27394 98.31717 90.89824 assigned negative charge : -287.6263 centred at (gu) : 91.62878 98.64007 90.66969 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 60299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17226 grid for indexing accessible points = 1.400000 m= 23064 mr = 41572 m= 3636 mr = 17857 m= 194 mr = 2364 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 987 time to turn everything in is 0.3400000 number of dielectric boundary points 25323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14453 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) : 0.6473316 object centre at (A) : 15.16250 22.29150 3.120501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3418717E-02 1.6576186E-02 midg,1,midg; midg,igrid,midg 3.0558605E-02 -5.5080261E-03 1,midg,midg; igrid,midg,midg 7.5213765E-03 -5.2046655E-03 gauss-seidel spectral radius is 0.9986094 estimated iterations to convergence 213 setup time was (sec) 0.5800000 now iterating at: 14:10:26 rms-change max change #iterations 3.702621 168.6581 at 10iterations 1.720040 62.96566 at 20iterations 0.8052279 30.33383 at 30iterations 0.3744935 13.39842 at 40iterations 0.1737383 5.979499 at 50iterations 8.0822930E-02 2.809662 at 60iterations 3.7469499E-02 1.307709 at 70iterations 1.7473057E-02 0.6457176 at 80iterations 8.1079612E-03 0.2848532 at 90iterations 3.7523592E-03 0.1484194 at 100iterations 1.7544947E-03 6.1783791E-02 at 110iterations 8.1501913E-04 2.6554108E-02 at 120iterations finished qdiffx linear iterations at : 14:10:42 total time elapsed so far: 8.850000 # loops : 120 mean,max change (kT/e) : 8.1501913E-04 2.6554108E-02 energy calculations done at 8.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.990000 DelPhi exited at 14:10:43 8.991u 0.241s 0:18.62 49.5% 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 Tue Nov 22 2011 at 14:10:44 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.912992 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): -5.079000 35.40400 ymin,ymax (A): -3.943000 48.52600 zmin,zma (A): -24.37700 30.61800 x,y,z range (A): 40.48300 52.46900 54.99500 scale (grids/A): 2.912992 object centre (A): 15.16250 22.29150 3.120501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 91.91091 102.4758 91.34749 assigned negative charge : -287.6263 centred at (gu) : 92.44313 102.9603 91.00455 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 138750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17226 grid for indexing accessible points = 1.400000 m= 72905 mr = 100014 m= 28472 mr = 60961 m= 6416 mr = 23886 m= 818 mr = 4884 m= 36 mr = 568 m= 0 mr = 8 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 3401 time to turn everything in is 0.8600000 number of dielectric boundary points 57076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14656 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) : 1.941995 object centre at (A) : 15.16250 22.29150 3.120501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.094067 5.3790722E-02 midg,1,midg; midg,igrid,midg 0.2944893 -9.0749666E-02 1,midg,midg; igrid,midg,midg 4.1896492E-02 -2.5453813E-02 gauss-seidel spectral radius is 0.9992378 estimated iterations to convergence 286 setup time was (sec) 1.140000 now iterating at: 14:10:46 rms-change max change #iterations 8.717141 458.4333 at 10iterations 5.000268 172.7411 at 20iterations 2.864377 58.12273 at 30iterations 1.630200 31.69674 at 40iterations 0.9324993 20.87062 at 50iterations 0.5313411 10.46158 at 60iterations 0.3023993 5.874962 at 70iterations 0.1716401 3.284479 at 80iterations 9.7848736E-02 1.982897 at 90iterations 5.5598520E-02 1.065933 at 100iterations 3.1651467E-02 0.5912323 at 110iterations 1.8046079E-02 0.3706856 at 120iterations 1.0224265E-02 0.2119751 at 130iterations 5.8215405E-03 0.1170802 at 140iterations 3.3171824E-03 6.1753273E-02 at 150iterations 1.8884301E-03 3.7626266E-02 at 160iterations 1.0724061E-03 2.0854950E-02 at 170iterations 6.1047450E-04 1.2357712E-02 at 180iterations finished qdiffx linear iterations at : 14:11:10 total time elapsed so far: 14.57000 # loops : 180 mean,max change (kT/e) : 6.1047450E-04 1.2357712E-02 energy calculations done at 14.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.71000 DelPhi exited at 14:11:11 14.710u 0.415s 0:27.53 54.9% 0+0k 0+0io 0pf+0w