Sat Oct 8 21:01:51 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 Sat Oct 8 2011 at 21:01:51 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 506 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6138248 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): -10.56100 39.08900 ymin,ymax (A): -22.39900 24.73900 zmin,zma (A): -12.60600 45.39100 x,y,z range (A): 49.65000 47.13800 57.99700 scale (grids/A): 0.6138248 object centre (A): 14.26400 1.170000 16.39250 number of atom coordinates read : 2602 total number of charged atoms : 2458 net assigned charge : 3.906008 assigned positive charge : 393.3991 centred at (gu) : 88.51685 89.51319 89.66747 assigned negative charge : -389.4936 centred at (gu) : 88.39350 89.55930 89.55163 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6350 nv = 96 ne = 84 npr = 54561 no. pairs analyzed = 54561 no. exposed pairs = 2986 no. arc points = 21275 no. surface atoms = 1005 nbur = 1597 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3552 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.2000000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7936 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0972732E-09 8.4246077E-09 midg,1,midg; midg,igrid,midg 5.8717320E-09 1.5115430E-10 1,midg,midg; igrid,midg,midg -5.9867244E-09 6.8263422E-09 gauss-seidel spectral radius is 0.9862518 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 21:01:51 rms-change max change #iterations 0.1250984 18.19486 at 10iterations 1.1209436E-02 1.768555 at 20iterations 1.0066042E-03 0.1652222 at 30iterations 9.0969668E-05 1.2699127E-02 at 40iterations 8.0496120E-06 1.2283325E-03 at 50iterations finished qdiffx linear iterations at : 21:01:54 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 8.0496120E-06 1.2283325E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 21:01:55 3.576u 0.188s 0:04.02 93.2% 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 Sat Oct 8 2011 at 21:01:55 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 506 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.841475 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): -10.56100 39.08900 ymin,ymax (A): -22.39900 24.73900 zmin,zma (A): -12.60600 45.39100 x,y,z range (A): 49.65000 47.13800 57.99700 scale (grids/A): 1.841475 object centre (A): 14.26400 1.170000 16.39250 number of atom coordinates read : 2602 total number of charged atoms : 2458 net assigned charge : 3.906008 assigned positive charge : 393.3991 centred at (gu) : 85.55042 88.53895 89.00208 assigned negative charge : -389.4936 centred at (gu) : 85.18041 88.67773 88.65472 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21275 grid for indexing accessible points = 1.400000 m= 23472 mr = 48739 m= 3082 mr = 17237 m= 121 mr = 1823 m= 0 mr = 44 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5173 time to turn everything in is 0.3400000 number of dielectric boundary points 28085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19265 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) : 0.6138248 object centre at (A) : 14.26400 1.170000 16.39250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4773682E-02 2.0940173E-02 midg,1,midg; midg,igrid,midg 1.3670645E-02 2.6405547E-03 1,midg,midg; igrid,midg,midg -8.3605554E-03 3.6605250E-02 gauss-seidel spectral radius is 0.9985361 estimated iterations to convergence 207 setup time was (sec) 0.5800000 now iterating at: 21:01:55 rms-change max change #iterations 3.946369 169.8089 at 10iterations 1.797897 63.22762 at 20iterations 0.8175250 28.46024 at 30iterations 0.3732270 12.42040 at 40iterations 0.1704688 5.846565 at 50iterations 7.7863581E-02 2.723949 at 60iterations 3.5515498E-02 1.141625 at 70iterations 1.6205698E-02 0.4933319 at 80iterations 7.3603913E-03 0.2585297 at 90iterations 3.3748213E-03 0.1168156 at 100iterations 1.5376601E-03 4.9103737E-02 at 110iterations 7.0164801E-04 2.2993088E-02 at 120iterations finished qdiffx linear iterations at : 21:02:03 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 7.0164801E-04 2.2993088E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 21:02:03 8.133u 0.206s 0:08.61 96.7% 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 Sat Oct 8 2011 at 21:02:03 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 506 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.762212 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): -10.56100 39.08900 ymin,ymax (A): -22.39900 24.73900 zmin,zma (A): -12.60600 45.39100 x,y,z range (A): 49.65000 47.13800 57.99700 scale (grids/A): 2.762212 object centre (A): 14.26400 1.170000 16.39250 number of atom coordinates read : 2602 total number of charged atoms : 2458 net assigned charge : 3.906008 assigned positive charge : 393.3991 centred at (gu) : 83.32563 87.80833 88.50291 assigned negative charge : -389.4936 centred at (gu) : 82.77062 88.01655 87.98207 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 160635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21275 grid for indexing accessible points = 1.400000 m= 78359 mr = 117912 m= 25347 mr = 64382 m= 5244 mr = 20232 m= 575 mr = 3861 m= 33 mr = 383 m= 0 mr = 18 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 17483 time to turn everything in is 0.8600000 number of dielectric boundary points 63405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 19655 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) : 1.841475 object centre at (A) : 14.26400 1.170000 16.39250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1882077E-02 0.2226936 midg,1,midg; midg,igrid,midg 0.1531722 3.0566782E-02 1,midg,midg; igrid,midg,midg -7.5931363E-02 0.5238571 gauss-seidel spectral radius is 0.9992242 estimated iterations to convergence 283 setup time was (sec) 1.110000 now iterating at: 21:02:05 rms-change max change #iterations 9.321725 279.8494 at 10iterations 5.324163 117.5436 at 20iterations 3.024209 58.06765 at 30iterations 1.717062 36.15627 at 40iterations 0.9728333 19.15076 at 50iterations 0.5528941 10.61077 at 60iterations 0.3127815 5.823387 at 70iterations 0.1769971 3.484602 at 80iterations 0.1003412 2.092957 at 90iterations 5.6902733E-02 1.059313 at 100iterations 3.2241087E-02 0.6476212 at 110iterations 1.8271402E-02 0.3408821 at 120iterations 1.0313744E-02 0.1976871 at 130iterations 5.8577135E-03 0.1076031 at 140iterations 3.3134974E-03 6.4893723E-02 at 150iterations 1.8769527E-03 3.5518646E-02 at 160iterations 1.0626180E-03 2.0151138E-02 at 170iterations 6.0244923E-04 1.1098862E-02 at 180iterations finished qdiffx linear iterations at : 21:02:17 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 6.0244923E-04 1.1098862E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 21:02:17 13.237u 0.235s 0:13.79 97.6% 0+0k 0+0io 0pf+0w