Tue Oct 11 04:30:01 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 Tue Oct 11 2011 at 04:30:01 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6388744 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): -12.37700 36.51600 ymin,ymax (A): -25.82100 22.59900 zmin,zma (A): -10.43100 45.29200 x,y,z range (A): 48.89300 48.42000 55.72300 scale (grids/A): 0.6388744 object centre (A): 12.06950 -1.611000 17.43050 number of atom coordinates read : 2731 total number of charged atoms : 2579 net assigned charge : 3.176012 assigned positive charge : 415.6428 centred at (gu) : 90.50495 90.26318 91.95595 assigned negative charge : -412.4673 centred at (gu) : 90.25306 90.09752 91.89267 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7388 nv = 96 ne = 84 npr = 55782 no. pairs analyzed = 55782 no. exposed pairs = 3304 no. arc points = 22789 no. surface atoms = 1108 nbur = 1623 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 4192 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.2000000 number of dielectric boundary points 3544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2237 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8914 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2310380E-09 1.7800854E-08 midg,1,midg; midg,igrid,midg -1.5169526E-08 2.4995508E-08 1,midg,midg; igrid,midg,midg -2.4062075E-08 3.7364739E-08 gauss-seidel spectral radius is 0.9873130 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 04:30:01 rms-change max change #iterations 0.1492530 20.36877 at 10iterations 1.5273601E-02 2.143421 at 20iterations 1.7428835E-03 0.2738152 at 30iterations 2.8590654E-04 3.7284851E-02 at 40iterations 7.3975403E-05 1.0318756E-02 at 50iterations finished qdiffx linear iterations at : 04:30:04 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.3975403E-05 1.0318756E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 04:30:05 3.397u 0.165s 0:03.88 91.4% 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 Tue Oct 11 2011 at 04:30:05 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.916623 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): -12.37700 36.51600 ymin,ymax (A): -25.82100 22.59900 zmin,zma (A): -10.43100 45.29200 x,y,z range (A): 48.89300 48.42000 55.72300 scale (grids/A): 1.916623 object centre (A): 12.06950 -1.611000 17.43050 number of atom coordinates read : 2731 total number of charged atoms : 2579 net assigned charge : 3.176012 assigned positive charge : 415.6428 centred at (gu) : 91.51431 90.78914 95.86726 assigned negative charge : -412.4673 centred at (gu) : 90.75890 90.29208 95.67765 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 28963 mr = 56526 m= 4301 mr = 21473 m= 242 mr = 2644 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 967 time to turn everything in is 0.3900000 number of dielectric boundary points 32665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20268 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) : 0.6388744 object centre at (A) : 12.06950 -1.611000 17.43050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6707107E-02 8.7997066E-03 midg,1,midg; midg,igrid,midg -1.0219947E-02 2.7242115E-02 1,midg,midg; igrid,midg,midg -9.6488185E-03 5.3622242E-02 gauss-seidel spectral radius is 0.9986621 estimated iterations to convergence 217 setup time was (sec) 0.6000000 now iterating at: 04:30:06 rms-change max change #iterations 4.481666 206.8002 at 10iterations 2.114571 78.89386 at 20iterations 1.001068 31.10317 at 30iterations 0.4742815 15.25321 at 40iterations 0.2237288 6.964573 at 50iterations 0.1055304 3.293987 at 60iterations 5.0019640E-02 1.750021 at 70iterations 2.3667727E-02 0.7967682 at 80iterations 1.1205966E-02 0.3698896 at 90iterations 5.3086253E-03 0.1679287 at 100iterations 2.5381560E-03 7.4640274E-02 at 110iterations 1.2159941E-03 3.7742615E-02 at 120iterations finished qdiffx linear iterations at : 04:30:13 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.2159941E-03 3.7742615E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 04:30:13 7.800u 0.192s 0:08.38 95.3% 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 Oct 11 2011 at 04:30:13 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.874935 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): -12.37700 36.51600 ymin,ymax (A): -25.82100 22.59900 zmin,zma (A): -10.43100 45.29200 x,y,z range (A): 48.89300 48.42000 55.72300 scale (grids/A): 2.874935 object centre (A): 12.06950 -1.611000 17.43050 number of atom coordinates read : 2731 total number of charged atoms : 2579 net assigned charge : 3.176012 assigned positive charge : 415.6428 centred at (gu) : 92.27145 91.18359 98.80067 assigned negative charge : -412.4673 centred at (gu) : 91.13820 90.43800 98.51641 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 184952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 94812 mr = 136865 m= 33199 mr = 78211 m= 7563 mr = 26676 m= 886 mr = 5516 m= 49 mr = 534 m= 0 mr = 12 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 3240 time to turn everything in is 1.000000 number of dielectric boundary points 73647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 20620 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) : 1.916623 object centre at (A) : 12.06950 -1.611000 17.43050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7136067 0.2812786 midg,1,midg; midg,igrid,midg -0.1232906 0.3213440 1,midg,midg; igrid,midg,midg -7.8081220E-02 0.4365393 gauss-seidel spectral radius is 0.9992655 estimated iterations to convergence 291 setup time was (sec) 1.240000 now iterating at: 04:30:15 rms-change max change #iterations 10.46848 307.9969 at 10iterations 6.125338 138.4912 at 20iterations 3.581463 71.24857 at 30iterations 2.086274 41.80680 at 40iterations 1.212083 24.95895 at 50iterations 0.7023907 12.66005 at 60iterations 0.4054222 7.999916 at 70iterations 0.2357327 4.465563 at 80iterations 0.1361714 2.451670 at 90iterations 7.8796342E-02 1.451521 at 100iterations 4.5494586E-02 0.8674412 at 110iterations 2.6367884E-02 0.5368576 at 120iterations 1.5261678E-02 0.2731094 at 130iterations 8.8657578E-03 0.1534290 at 140iterations 5.1827664E-03 8.9500427E-02 at 150iterations 3.0530256E-03 5.4580927E-02 at 160iterations 1.8214494E-03 3.8902283E-02 at 170iterations 1.1172672E-03 2.2605896E-02 at 180iterations finished qdiffx linear iterations at : 04:30:26 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 1.1172672E-03 2.2605896E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 04:30:26 12.689u 0.210s 0:13.18 97.7% 0+0k 0+0io 0pf+0w