Mon Oct 10 17:15:59 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 17:15:59 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: 380 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5103943 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): -18.35400 36.66900 ymin,ymax (A): -32.31200 35.08000 zmin,zma (A): -3.998000 65.75200 x,y,z range (A): 55.02300 67.39200 69.75000 scale (grids/A): 0.5103943 object centre (A): 9.157501 1.384001 30.87700 number of atom coordinates read : 4786 total number of charged atoms : 4578 net assigned charge : 3.306034 assigned positive charge : 724.2123 centred at (gu) : 90.24022 90.63459 88.30146 assigned negative charge : -720.9109 centred at (gu) : 90.15054 90.66364 88.35722 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7768 nv = 96 ne = 84 npr = 96931 no. pairs analyzed = 96931 no. exposed pairs = 6267 no. arc points = 43042 no. surface atoms = 2079 nbur = 2707 mkacc time = 0.2300000 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 = 1.680000 m= 299 mr = 3909 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4127 ## 600 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 10513 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9418834E-10 -6.4258716E-11 midg,1,midg; midg,igrid,midg 1.0028090E-10 -3.8193483E-11 1,midg,midg; igrid,midg,midg -1.7916783E-10 2.9078073E-10 gauss-seidel spectral radius is 0.9803686 estimated iterations to convergence 59 setup time was (sec) 0.7400000 now iterating at: 17:16:00 rms-change max change #iterations 6.7990869E-02 10.56231 at 10iterations 3.9284164E-03 0.5718002 at 20iterations 3.5608769E-04 5.3441048E-02 at 30iterations 1.0056663E-04 1.4003754E-02 at 40iterations 4.0616571E-05 6.6094398E-03 at 50iterations finished qdiffx linear iterations at : 17:16:02 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 4.0616571E-05 6.6094398E-03 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 17:16:03 3.806u 0.202s 0:04.47 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 17:16:03 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: 380 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.531183 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): -18.35400 36.66900 ymin,ymax (A): -32.31200 35.08000 zmin,zma (A): -3.998000 65.75200 x,y,z range (A): 55.02300 67.39200 69.75000 scale (grids/A): 1.531183 object centre (A): 9.157501 1.384001 30.87700 number of atom coordinates read : 4786 total number of charged atoms : 4578 net assigned charge : 3.306034 assigned positive charge : 724.2123 centred at (gu) : 90.71911 91.90276 84.90298 assigned negative charge : -720.9109 centred at (gu) : 90.45138 91.99091 85.07135 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 88164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43042 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25404 mr = 59817 m= 2274 mr = 16543 m= 44 mr = 897 m= 0 mr = 1 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.6900000 number of dielectric boundary points 38628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 546 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 34459 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) : 0.5103943 object centre at (A) : 9.157501 1.384001 30.87700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3149919E-03 -5.5280169E-03 midg,1,midg; midg,igrid,midg -1.9813820E-03 -5.5405791E-03 1,midg,midg; igrid,midg,midg -1.3099351E-03 1.0268183E-02 gauss-seidel spectral radius is 0.9981118 estimated iterations to convergence 183 setup time was (sec) 1.010000 now iterating at: 17:16:04 rms-change max change #iterations 3.804032 156.0827 at 10iterations 1.560034 55.99643 at 20iterations 0.6388098 20.93869 at 30iterations 0.2627577 9.479637 at 40iterations 0.1076364 4.396763 at 50iterations 4.4224147E-02 1.508478 at 60iterations 1.8158289E-02 0.6333199 at 70iterations 7.4846004E-03 0.2405977 at 80iterations 3.0883667E-03 0.1043539 at 90iterations 1.2786733E-03 4.7485352E-02 at 100iterations 5.3648121E-04 1.7629623E-02 at 110iterations 2.3551717E-04 8.0893040E-03 at 120iterations finished qdiffx linear iterations at : 17:16:12 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 2.3551717E-04 8.0893040E-03 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 17:16:12 8.484u 0.247s 0:09.21 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 17:16:12 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: 380 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.296774 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): -18.35400 36.66900 ymin,ymax (A): -32.31200 35.08000 zmin,zma (A): -3.998000 65.75200 x,y,z range (A): 55.02300 67.39200 69.75000 scale (grids/A): 2.296774 object centre (A): 9.157501 1.384001 30.87700 number of atom coordinates read : 4786 total number of charged atoms : 4578 net assigned charge : 3.306034 assigned positive charge : 724.2123 centred at (gu) : 91.07841 92.85364 82.35398 assigned negative charge : -720.9109 centred at (gu) : 90.67709 92.98640 82.60705 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 205373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43042 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90597 mr = 147074 m= 22679 mr = 70071 m= 3169 mr = 15780 m= 153 mr = 1834 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 1.640000 number of dielectric boundary points 87163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 36525 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) : 1.531183 object centre at (A) : 9.157501 1.384001 30.87700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1336776 -0.1537486 midg,1,midg; midg,igrid,midg -8.2661457E-02 -0.1702601 1,midg,midg; igrid,midg,midg -1.9525731E-02 0.1589154 gauss-seidel spectral radius is 0.9991640 estimated iterations to convergence 273 setup time was (sec) 1.980000 now iterating at: 17:16:15 rms-change max change #iterations 10.38989 272.2198 at 10iterations 5.977702 134.6899 at 20iterations 3.394908 74.84367 at 30iterations 1.923041 47.82474 at 40iterations 1.084577 25.60454 at 50iterations 0.6097515 14.42134 at 60iterations 0.3419259 7.547657 at 70iterations 0.1915195 4.676358 at 80iterations 0.1068638 2.211832 at 90iterations 5.9704810E-02 1.219486 at 100iterations 3.3318207E-02 0.6173210 at 110iterations 1.8502042E-02 0.3593369 at 120iterations 1.0317557E-02 0.2017980 at 130iterations 5.7494640E-03 0.1184998 at 140iterations 3.2004938E-03 5.9145927E-02 at 150iterations 1.7832132E-03 3.3298969E-02 at 160iterations 9.9580653E-04 2.0733833E-02 at 170iterations 5.5861037E-04 1.0772228E-02 at 180iterations finished qdiffx linear iterations at : 17:16:27 total time elapsed so far: 14.00000 # loops : 180 mean,max change (kT/e) : 5.5861037E-04 1.0772228E-02 energy calculations done at 14.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.18000 DelPhi exited at 17:16:27 14.180u 0.268s 0:14.82 97.4% 0+0k 0+0io 0pf+0w