Mon Oct 10 17:03:55 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 17:03:55 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4294 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5103504 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): -15.57900 36.58000 ymin,ymax (A): -32.23200 31.38000 zmin,zma (A): -3.937000 65.81900 x,y,z range (A): 52.15900 63.61200 69.75600 scale (grids/A): 0.5103504 object centre (A): 10.50050 -0.4259996 30.94100 number of atom coordinates read : 4294 total number of charged atoms : 4046 net assigned charge : 3.206027 assigned positive charge : 637.4683 centred at (gu) : 90.13102 90.75527 87.56667 assigned negative charge : -634.2662 centred at (gu) : 90.00581 90.82175 87.60461 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7068 nv = 96 ne = 84 npr = 87213 no. pairs analyzed = 87213 no. exposed pairs = 5576 no. arc points = 38552 no. surface atoms = 1869 nbur = 2425 mkacc time = 0.2200000 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 = 1.652000 m= 269 mr = 3584 m= 0 mr = 10 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3699 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9458 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4675564E-10 -2.1867185E-11 midg,1,midg; midg,igrid,midg 1.5755210E-10 -1.3311653E-10 1,midg,midg; igrid,midg,midg -2.3596144E-10 3.3309072E-10 gauss-seidel spectral radius is 0.9803321 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:03:56 rms-change max change #iterations 6.4559348E-02 9.734003 at 10iterations 3.5887002E-03 0.5403519 at 20iterations 2.3397096E-04 3.6209106E-02 at 30iterations 4.0664545E-05 6.4640045E-03 at 40iterations 1.4394809E-05 2.4113655E-03 at 50iterations finished qdiffx linear iterations at : 17:04:00 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 1.4394809E-05 2.4113655E-03 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 17:04:01 4.623u 0.428s 0:05.96 84.5% 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 Mon Oct 10 2011 at 17:04:01 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4294 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.531051 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): -15.57900 36.58000 ymin,ymax (A): -32.23200 31.38000 zmin,zma (A): -3.937000 65.81900 x,y,z range (A): 52.15900 63.61200 69.75600 scale (grids/A): 1.531051 object centre (A): 10.50050 -0.4259996 30.94100 number of atom coordinates read : 4294 total number of charged atoms : 4046 net assigned charge : 3.206027 assigned positive charge : 637.4683 centred at (gu) : 90.39185 92.26451 82.69911 assigned negative charge : -634.2662 centred at (gu) : 90.01715 92.46481 82.81370 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 79852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38552 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22899 mr = 54266 m= 2055 mr = 15048 m= 39 mr = 818 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 189 time to turn everything in is 0.6800000 number of dielectric boundary points 34713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 513 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 30376 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) : 0.5103504 object centre at (A) : 10.50050 -0.4259996 30.94100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6659292E-03 7.5659063E-03 midg,1,midg; midg,igrid,midg -2.8742889E-03 -1.1983897E-02 1,midg,midg; igrid,midg,midg -3.2409702E-03 9.3237311E-03 gauss-seidel spectral radius is 0.9980649 estimated iterations to convergence 181 setup time was (sec) 1.010000 now iterating at: 17:04:02 rms-change max change #iterations 3.540703 197.7519 at 10iterations 1.425027 52.44763 at 20iterations 0.5775705 19.61428 at 30iterations 0.2334943 8.747355 at 40iterations 9.5195241E-02 3.142804 at 50iterations 3.8544290E-02 1.295280 at 60iterations 1.5671728E-02 0.5481510 at 70iterations 6.3824621E-03 0.1970673 at 80iterations 2.6024336E-03 8.7400436E-02 at 90iterations 1.0717927E-03 3.7006378E-02 at 100iterations 4.5235574E-04 1.4138222E-02 at 110iterations 2.0250630E-04 8.1944466E-03 at 120iterations finished qdiffx linear iterations at : 17:04:12 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 2.0250630E-04 8.1944466E-03 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 17:04:14 10.649u 0.423s 0:12.69 87.1% 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 17:04:14 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4294 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.296577 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): -15.57900 36.58000 ymin,ymax (A): -32.23200 31.38000 zmin,zma (A): -3.937000 65.81900 x,y,z range (A): 52.15900 63.61200 69.75600 scale (grids/A): 2.296577 object centre (A): 10.50050 -0.4259996 30.94100 number of atom coordinates read : 4294 total number of charged atoms : 4046 net assigned charge : 3.206027 assigned positive charge : 637.4683 centred at (gu) : 90.58717 93.39649 79.04822 assigned negative charge : -634.2662 centred at (gu) : 90.02564 93.69733 79.22055 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 186316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38552 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 82198 mr = 133601 m= 20478 mr = 63815 m= 2850 mr = 14417 m= 149 mr = 1678 m= 0 mr = 36 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 651 time to turn everything in is 1.620000 number of dielectric boundary points 78444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 32273 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) : 1.531051 object centre at (A) : 10.50050 -0.4259996 30.94100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2216770 0.2337469 midg,1,midg; midg,igrid,midg -0.1134947 -0.2815647 1,midg,midg; igrid,midg,midg -5.0159112E-02 0.1403506 gauss-seidel spectral radius is 0.9991382 estimated iterations to convergence 269 setup time was (sec) 1.960000 now iterating at: 17:04:16 rms-change max change #iterations 9.627976 292.8459 at 10iterations 5.482183 135.3257 at 20iterations 3.091311 73.60015 at 30iterations 1.733622 36.95354 at 40iterations 0.9715132 25.25832 at 50iterations 0.5406891 12.53707 at 60iterations 0.3005459 6.757383 at 70iterations 0.1666675 3.438740 at 80iterations 9.2300206E-02 2.177165 at 90iterations 5.0921991E-02 0.9864388 at 100iterations 2.8180107E-02 0.5397271 at 110iterations 1.5557623E-02 0.3456612 at 120iterations 8.5942987E-03 0.1861850 at 130iterations 4.7452562E-03 0.1091928 at 140iterations 2.6136753E-03 5.9218407E-02 at 150iterations 1.4412892E-03 2.9916763E-02 at 160iterations 7.9576793E-04 1.5620708E-02 at 170iterations 4.4044905E-04 9.2430115E-03 at 180iterations finished qdiffx linear iterations at : 17:04:32 total time elapsed so far: 17.96000 # loops : 180 mean,max change (kT/e) : 4.4044905E-04 9.2430115E-03 energy calculations done at 17.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.12000 DelPhi exited at 17:04:33 18.129u 0.481s 0:19.47 95.5% 0+0k 0+0io 0pf+0w