Tue Nov 22 14:18:41 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 14:18:46 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: ASL 181 has a net charge of -0.1000 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: 0.5945125 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): -35.33000 9.940000 ymin,ymax (A): 1.485000 41.15500 zmin,zma (A): -1.884000 57.99700 x,y,z range (A): 45.27000 39.67000 59.88100 scale (grids/A): 0.5945125 object centre (A): -12.69500 21.32000 28.05650 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.900004 assigned positive charge : 294.0000 centred at (gu) : 90.53123 89.46006 89.79152 assigned negative charge : -291.1003 centred at (gu) : 90.46107 89.56991 89.78088 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4676 nv = 96 ne = 84 npr = 40478 no. pairs analyzed = 40478 no. exposed pairs = 2459 no. arc points = 17073 no. surface atoms = 835 nbur = 1135 mkacc time = 7.0000008E-02 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= 206 mr = 2543 m= 0 mr = 27 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2312 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1779 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0507878E-10 1.2026725E-09 midg,1,midg; midg,igrid,midg 3.9818744E-09 -1.3620997E-09 1,midg,midg; igrid,midg,midg -5.3904720E-10 2.9593057E-09 gauss-seidel spectral radius is 0.9853063 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 14:18:49 rms-change max change #iterations 8.9280270E-02 16.08914 at 10iterations 7.3389225E-03 1.581863 at 20iterations 6.0504372E-04 9.7620010E-02 at 30iterations 4.9723658E-05 8.5415840E-03 at 40iterations 4.0051877E-06 7.8201294E-04 at 50iterations finished qdiffx linear iterations at : 14:18:59 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 4.0051877E-06 7.8201294E-04 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 14:19:02 3.788u 0.211s 0:17.09 23.3% 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 14:19:05 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: ASL 181 has a net charge of -0.1000 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: 1.783537 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): -35.33000 9.940000 ymin,ymax (A): 1.485000 41.15500 zmin,zma (A): -1.884000 57.99700 x,y,z range (A): 45.27000 39.67000 59.88100 scale (grids/A): 1.783537 object centre (A): -12.69500 21.32000 28.05650 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.900004 assigned positive charge : 294.0000 centred at (gu) : 91.59376 88.38013 89.37463 assigned negative charge : -291.1003 centred at (gu) : 91.38342 88.70990 89.34277 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 50371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17073 grid for indexing accessible points = 1.400000 m= 17884 mr = 34342 m= 2375 mr = 13467 m= 89 mr = 1472 m= 0 mr = 27 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 442 time to turn everything in is 0.2700000 number of dielectric boundary points 21411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14299 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) : 0.5945125 object centre at (A) : -12.69500 21.32000 28.05650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8242517E-02 2.2087626E-02 midg,1,midg; midg,igrid,midg 7.9187070E-04 -6.6934903E-03 1,midg,midg; igrid,midg,midg -1.4461540E-03 -1.0162292E-03 gauss-seidel spectral radius is 0.9983675 estimated iterations to convergence 196 setup time was (sec) 0.5200000 now iterating at: 14:19:09 rms-change max change #iterations 3.187269 139.9414 at 10iterations 1.388272 61.13649 at 20iterations 0.6089698 24.21313 at 30iterations 0.2637712 9.979769 at 40iterations 0.1147825 4.923773 at 50iterations 5.0123166E-02 1.920265 at 60iterations 2.1798262E-02 0.8524384 at 70iterations 9.4997939E-03 0.4176941 at 80iterations 4.1588331E-03 0.1518250 at 90iterations 1.8152506E-03 7.1552753E-02 at 100iterations 7.9138158E-04 2.9995322E-02 at 110iterations 3.4438385E-04 1.4068604E-02 at 120iterations finished qdiffx linear iterations at : 14:19:32 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 3.4438385E-04 1.4068604E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 14:19:33 8.194u 0.241s 0:29.19 28.8% 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 14:19:35 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: ASL 181 has a net charge of -0.1000 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: 2.675306 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): -35.33000 9.940000 ymin,ymax (A): 1.485000 41.15500 zmin,zma (A): -1.884000 57.99700 x,y,z range (A): 45.27000 39.67000 59.88100 scale (grids/A): 2.675306 object centre (A): -12.69500 21.32000 28.05650 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.900004 assigned positive charge : 294.0000 centred at (gu) : 92.39056 87.57021 89.06183 assigned negative charge : -291.1003 centred at (gu) : 92.07509 88.06495 89.01421 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 116421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17073 grid for indexing accessible points = 1.400000 m= 58727 mr = 83230 m= 20290 mr = 48385 m= 4109 mr = 16673 m= 485 mr = 3095 m= 13 mr = 341 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1561 time to turn everything in is 0.6800000 number of dielectric boundary points 48321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14703 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) : 1.783537 object centre at (A) : -12.69500 21.32000 28.05650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2711625 0.1402461 midg,1,midg; midg,igrid,midg -2.9763240E-02 -9.5516592E-02 1,midg,midg; igrid,midg,midg -4.1853461E-02 -5.5694450E-02 gauss-seidel spectral radius is 0.9991616 estimated iterations to convergence 273 setup time was (sec) 0.9600000 now iterating at: 14:19:41 rms-change max change #iterations 7.723750 323.9221 at 10iterations 4.324042 120.2619 at 20iterations 2.422787 56.68338 at 30iterations 1.347480 29.32822 at 40iterations 0.7475718 16.92165 at 50iterations 0.4159335 9.108463 at 60iterations 0.2302537 5.981573 at 70iterations 0.1276274 2.658504 at 80iterations 7.0542134E-02 1.465569 at 90iterations 3.9000347E-02 0.8113480 at 100iterations 2.1661429E-02 0.4811077 at 110iterations 1.1971005E-02 0.2658658 at 120iterations 6.6155000E-03 0.1492188 at 130iterations 3.6605126E-03 8.9208603E-02 at 140iterations 2.0249118E-03 4.8839569E-02 at 150iterations 1.1232540E-03 2.7563095E-02 at 160iterations 6.1840529E-04 1.3786316E-02 at 170iterations 3.4228351E-04 7.5321198E-03 at 180iterations finished qdiffx linear iterations at : 14:20:19 total time elapsed so far: 13.61000 # loops : 180 mean,max change (kT/e) : 3.4228351E-04 7.5321198E-03 energy calculations done at 13.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.75000 DelPhi exited at 14:20:22 13.752u 0.278s 0:46.95 29.8% 0+0k 0+0io 0pf+0w