Mon Oct 10 17:00:24 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 17:00:24 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 = 4624 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5144509 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): -17.70200 36.58200 ymin,ymax (A): -30.61200 31.41000 zmin,zma (A): -3.809000 65.39100 x,y,z range (A): 54.28400 62.02200 69.20000 scale (grids/A): 0.5144509 object centre (A): 9.440001 0.3990002 30.79100 number of atom coordinates read : 4624 total number of charged atoms : 4376 net assigned charge : 9.206047 assigned positive charge : 692.9318 centred at (gu) : 90.31674 90.66598 88.14308 assigned negative charge : -683.7299 centred at (gu) : 90.21745 90.69627 88.11388 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7661 nv = 96 ne = 84 npr = 93654 no. pairs analyzed = 93654 no. exposed pairs = 6004 no. arc points = 41273 no. surface atoms = 2008 nbur = 2616 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 = 1.652000 m= 272 mr = 3895 m= 0 mr = 5 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3988 ## 626 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10274 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1048006E-10 1.4959005E-10 midg,1,midg; midg,igrid,midg 2.0517819E-10 7.8890998E-11 1,midg,midg; igrid,midg,midg -1.2544761E-10 4.7907289E-10 gauss-seidel spectral radius is 0.9806638 estimated iterations to convergence 59 setup time was (sec) 0.5100000 now iterating at: 17:00:25 rms-change max change #iterations 6.9556825E-02 11.07677 at 10iterations 4.0998249E-03 0.6033859 at 20iterations 4.4506785E-04 5.9076309E-02 at 30iterations 1.5002888E-04 2.1469012E-02 at 40iterations 6.0070870E-05 8.4615946E-03 at 50iterations finished qdiffx linear iterations at : 17:00:28 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 6.0070870E-05 8.4615946E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 17:00:28 3.554u 0.169s 0:04.14 89.6% 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 17:00:28 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 = 4624 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.543353 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): -17.70200 36.58200 ymin,ymax (A): -30.61200 31.41000 zmin,zma (A): -3.809000 65.39100 x,y,z range (A): 54.28400 62.02200 69.20000 scale (grids/A): 1.543353 object centre (A): 9.440001 0.3990002 30.79100 number of atom coordinates read : 4624 total number of charged atoms : 4376 net assigned charge : 9.206047 assigned positive charge : 692.9318 centred at (gu) : 90.94907 91.99636 84.42760 assigned negative charge : -683.7299 centred at (gu) : 90.65218 92.08843 84.34133 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 86616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41273 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24894 mr = 58820 m= 2173 mr = 16566 m= 54 mr = 869 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 37480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 567 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 33002 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) : 0.5144509 object centre at (A) : 9.440001 0.3990002 30.79100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3329312E-03 2.0290488E-02 midg,1,midg; midg,igrid,midg 6.3738674E-03 -7.0416927E-03 1,midg,midg; igrid,midg,midg -5.6979893E-04 1.1647313E-02 gauss-seidel spectral radius is 0.9981295 estimated iterations to convergence 184 setup time was (sec) 0.6500000 now iterating at: 17:00:29 rms-change max change #iterations 3.763647 156.0524 at 10iterations 1.544302 57.19178 at 20iterations 0.6349542 20.12015 at 30iterations 0.2621132 8.766502 at 40iterations 0.1079614 3.516644 at 50iterations 4.4637714E-02 1.479434 at 60iterations 1.8328883E-02 0.6320934 at 70iterations 7.5916997E-03 0.2380085 at 80iterations 3.1464468E-03 0.1059914 at 90iterations 1.3212272E-03 4.5315742E-02 at 100iterations 5.6604395E-04 1.9852638E-02 at 110iterations 2.5840540E-04 8.9530945E-03 at 120iterations finished qdiffx linear iterations at : 17:00:36 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 2.5840540E-04 8.9530945E-03 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 17:00:37 7.989u 0.208s 0:08.52 96.0% 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 17:00:37 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 = 4624 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.315029 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): -17.70200 36.58200 ymin,ymax (A): -30.61200 31.41000 zmin,zma (A): -3.809000 65.39100 x,y,z range (A): 54.28400 62.02200 69.20000 scale (grids/A): 2.315029 object centre (A): 9.440001 0.3990002 30.79100 number of atom coordinates read : 4624 total number of charged atoms : 4376 net assigned charge : 9.206047 assigned positive charge : 692.9318 centred at (gu) : 91.42329 92.99409 81.64126 assigned negative charge : -683.7299 centred at (gu) : 90.97817 93.13248 81.51194 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 201757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41273 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 88923 mr = 144851 m= 22054 mr = 68907 m= 3098 mr = 15636 m= 184 mr = 1887 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 84677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 34903 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) : 1.543353 object centre at (A) : 9.440001 0.3990002 30.79100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1463992 0.4593103 midg,1,midg; midg,igrid,midg 8.1268132E-02 -0.1965499 1,midg,midg; igrid,midg,midg -1.4288972E-02 0.1640841 gauss-seidel spectral radius is 0.9991655 estimated iterations to convergence 273 setup time was (sec) 1.280000 now iterating at: 17:00:38 rms-change max change #iterations 10.17942 363.1290 at 10iterations 5.851939 133.0442 at 20iterations 3.333541 71.41632 at 30iterations 1.889814 40.93488 at 40iterations 1.067069 26.36481 at 50iterations 0.5999432 15.71117 at 60iterations 0.3371858 7.139202 at 70iterations 0.1891527 3.685764 at 80iterations 0.1058410 2.074741 at 90iterations 5.9104376E-02 1.123594 at 100iterations 3.3027429E-02 0.6916695 at 110iterations 1.8390559E-02 0.3826771 at 120iterations 1.0257853E-02 0.1863708 at 130iterations 5.7202312E-03 0.1124258 at 140iterations 3.1937356E-03 6.1861992E-02 at 150iterations 1.7854831E-03 3.4290314E-02 at 160iterations 1.0054805E-03 2.3324490E-02 at 170iterations 5.7077530E-04 1.1642456E-02 at 180iterations finished qdiffx linear iterations at : 17:00:50 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 5.7077530E-04 1.1642456E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 17:00:50 13.037u 0.222s 0:13.70 96.7% 0+0k 0+0io 0pf+0w