Mon Oct 10 16:59:42 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+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 Mon Oct 10 2011 at 16:59:42 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5425093 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): -47.50300 2.005000 ymin,ymax (A): -67.20900 -1.588000 zmin,zma (A): -29.37100 19.24400 x,y,z range (A): 49.50800 65.62100 48.61500 scale (grids/A): 0.5425093 object centre (A): -22.74900 -34.39850 -5.063500 number of atom coordinates read : 2647 total number of charged atoms : 2472 net assigned charge : 6.806020 assigned positive charge : 390.8568 centred at (gu) : 90.20416 90.41127 89.45377 assigned negative charge : -384.0517 centred at (gu) : 90.09473 90.24283 89.41408 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5175 nv = 96 ne = 84 npr = 52661 no. pairs analyzed = 52661 no. exposed pairs = 3543 no. arc points = 25292 no. surface atoms = 1192 nbur = 1455 mkacc time = 0.1500000 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 = 1.568000 m= 223 mr = 2579 m= 0 mr = 7 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 2812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2513 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 6648 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8776712E-10 4.9507676E-10 midg,1,midg; midg,igrid,midg -4.4943463E-10 1.3278590E-09 1,midg,midg; igrid,midg,midg -1.8187692E-10 9.5831543E-10 gauss-seidel spectral radius is 0.9824643 estimated iterations to convergence 62 setup time was (sec) 0.6300000 now iterating at: 16:59:42 rms-change max change #iterations 6.7638643E-02 11.29256 at 10iterations 4.4687702E-03 0.7938387 at 20iterations 3.4491782E-04 5.5619240E-02 at 30iterations 4.0979736E-05 7.3757172E-03 at 40iterations 6.7496103E-06 1.3179779E-03 at 50iterations finished qdiffx linear iterations at : 16:59:45 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.7496103E-06 1.3179779E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 16:59:46 3.515u 0.149s 0:04.08 89.4% 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 Mon Oct 10 2011 at 16:59:46 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 1.627528 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): -47.50300 2.005000 ymin,ymax (A): -67.20900 -1.588000 zmin,zma (A): -29.37100 19.24400 x,y,z range (A): 49.50800 65.62100 48.61500 scale (grids/A): 1.627528 object centre (A): -22.74900 -34.39850 -5.063500 number of atom coordinates read : 2647 total number of charged atoms : 2472 net assigned charge : 6.806020 assigned positive charge : 390.8568 centred at (gu) : 90.61203 91.23300 88.36086 assigned negative charge : -384.0517 centred at (gu) : 90.28427 90.72817 88.24227 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 56946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25292 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17897 mr = 37757 m= 1852 mr = 11894 m= 61 mr = 783 m= 0 mr = 8 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 26314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 307 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 18895 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) : 0.5425093 object centre at (A) : -22.74900 -34.39850 -5.063500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2119506E-04 5.6850291E-03 midg,1,midg; midg,igrid,midg -1.0476198E-02 2.5300970E-02 1,midg,midg; igrid,midg,midg -5.3521111E-03 8.1641600E-03 gauss-seidel spectral radius is 0.9981413 estimated iterations to convergence 184 setup time was (sec) 0.7400000 now iterating at: 16:59:47 rms-change max change #iterations 3.072719 158.3027 at 10iterations 1.268166 52.93932 at 20iterations 0.5221061 21.31065 at 30iterations 0.2157108 8.435493 at 40iterations 8.9276403E-02 3.621262 at 50iterations 3.6747627E-02 1.453869 at 60iterations 1.5130222E-02 0.5802855 at 70iterations 6.2677194E-03 0.2287083 at 80iterations 2.5782951E-03 0.1013536 at 90iterations 1.0703115E-03 4.1486263E-02 at 100iterations 4.4347363E-04 1.6854286E-02 at 110iterations 1.8437119E-04 7.0588589E-03 at 120iterations finished qdiffx linear iterations at : 16:59:53 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 1.8437119E-04 7.0588589E-03 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 16:59:54 7.435u 0.179s 0:08.03 94.6% 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 16:59:54 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.441292 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): -47.50300 2.005000 ymin,ymax (A): -67.20900 -1.588000 zmin,zma (A): -29.37100 19.24400 x,y,z range (A): 49.50800 65.62100 48.61500 scale (grids/A): 2.441292 object centre (A): -22.74900 -34.39850 -5.063500 number of atom coordinates read : 2647 total number of charged atoms : 2472 net assigned charge : 6.806020 assigned positive charge : 390.8568 centred at (gu) : 90.91789 91.84938 87.54110 assigned negative charge : -384.0517 centred at (gu) : 90.42636 91.09212 87.36331 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 132205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25292 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61180 mr = 92639 m= 17719 mr = 47649 m= 2719 mr = 12711 m= 179 mr = 1551 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 59391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 19742 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) : 1.627528 object centre at (A) : -22.74900 -34.39850 -5.063500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5916733E-02 7.1690783E-02 midg,1,midg; midg,igrid,midg -0.1351929 0.4133568 1,midg,midg; igrid,midg,midg -5.9990767E-02 0.1050112 gauss-seidel spectral radius is 0.9991217 estimated iterations to convergence 267 setup time was (sec) 1.350000 now iterating at: 16:59:55 rms-change max change #iterations 7.962785 319.5896 at 10iterations 4.450530 157.9087 at 20iterations 2.465744 60.04447 at 30iterations 1.360393 34.13539 at 40iterations 0.7492774 18.03891 at 50iterations 0.4117015 9.479281 at 60iterations 0.2253095 4.787003 at 70iterations 0.1233792 2.719627 at 80iterations 6.7481309E-02 1.445299 at 90iterations 3.6978066E-02 0.9065857 at 100iterations 2.0242222E-02 0.4943886 at 110iterations 1.1009843E-02 0.2464952 at 120iterations 6.0115359E-03 0.1279831 at 130iterations 3.2892176E-03 7.2540283E-02 at 140iterations 1.7948933E-03 4.1978300E-02 at 150iterations 9.7671431E-04 2.0404816E-02 at 160iterations 5.3414644E-04 1.0920763E-02 at 170iterations 2.9196203E-04 6.0752630E-03 at 180iterations finished qdiffx linear iterations at : 17:00:05 total time elapsed so far: 11.42000 # loops : 180 mean,max change (kT/e) : 2.9196203E-04 6.0752630E-03 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 17:00:06 11.636u 0.195s 0:12.16 97.2% 0+0k 0+0io 0pf+0w