Mon Oct 10 17:07:41 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 17:07:41 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3689 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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: 0.5575131 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): -30.01000 33.84500 ymin,ymax (A): -31.51900 31.33500 zmin,zma (A): 29.12400 86.44600 x,y,z range (A): 63.85500 62.85400 57.32200 scale (grids/A): 0.5575131 object centre (A): 1.917500 -9.2000008E-02 57.78500 number of atom coordinates read : 3689 total number of charged atoms : 3491 net assigned charge : 5.706039 assigned positive charge : 555.3007 centred at (gu) : 89.99186 91.69019 91.22350 assigned negative charge : -549.5964 centred at (gu) : 90.11876 91.70986 91.22869 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7340 nv = 96 ne = 84 npr = 75521 no. pairs analyzed = 75521 no. exposed pairs = 4760 no. arc points = 33159 no. surface atoms = 1585 nbur = 2104 mkacc time = 0.1600000 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 = 1.540000 m= 288 mr = 3728 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3333 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9563 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6611282E-10 6.5611189E-10 midg,1,midg; midg,igrid,midg 5.3718646E-10 4.5708207E-10 1,midg,midg; igrid,midg,midg 2.1187330E-09 -1.0487491E-09 gauss-seidel spectral radius is 0.9834586 estimated iterations to convergence 64 setup time was (sec) 0.5600000 now iterating at: 17:07:42 rms-change max change #iterations 9.1906622E-02 12.32871 at 10iterations 6.7100157E-03 1.007889 at 20iterations 6.5681688E-04 9.1131210E-02 at 30iterations 1.3182666E-04 2.1329880E-02 at 40iterations 3.5145156E-05 5.7601929E-03 at 50iterations finished qdiffx linear iterations at : 17:07:44 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 3.5145156E-05 5.7601929E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 17:07:45 3.148u 0.145s 0:03.69 88.8% 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 17:07:45 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3689 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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: 1.672539 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): -30.01000 33.84500 ymin,ymax (A): -31.51900 31.33500 zmin,zma (A): 29.12400 86.44600 x,y,z range (A): 63.85500 62.85400 57.32200 scale (grids/A): 1.672539 object centre (A): 1.917500 -9.2000008E-02 57.78500 number of atom coordinates read : 3689 total number of charged atoms : 3491 net assigned charge : 5.706039 assigned positive charge : 555.3007 centred at (gu) : 89.97431 95.06960 93.66951 assigned negative charge : -549.5964 centred at (gu) : 90.35590 95.12896 93.68562 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33159 grid for indexing accessible points = 1.400000 m= 24946 mr = 54599 m= 2714 mr = 16869 m= 86 mr = 1323 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.5500000 number of dielectric boundary points 35656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 26865 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) : 0.5575131 object centre at (A) : 1.917500 -9.2000008E-02 57.78500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9727733E-03 4.8648836E-03 midg,1,midg; midg,igrid,midg -3.6392964E-03 2.1592593E-04 1,midg,midg; igrid,midg,midg 2.2866532E-02 -5.1997039E-03 gauss-seidel spectral radius is 0.9983407 estimated iterations to convergence 195 setup time was (sec) 0.8000000 now iterating at: 17:07:46 rms-change max change #iterations 3.962637 158.7487 at 10iterations 1.713912 59.06628 at 20iterations 0.7412884 25.66278 at 30iterations 0.3205374 10.56744 at 40iterations 0.1385333 4.768856 at 50iterations 6.0083605E-02 2.035000 at 60iterations 2.6087331E-02 0.8193245 at 70iterations 1.1328238E-02 0.3640747 at 80iterations 4.9329340E-03 0.1567841 at 90iterations 2.1795314E-03 7.6045990E-02 at 100iterations 9.7590795E-04 3.4755707E-02 at 110iterations 4.4921911E-04 1.5048981E-02 at 120iterations finished qdiffx linear iterations at : 17:07:52 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 4.4921911E-04 1.5048981E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 17:07:53 7.063u 0.184s 0:08.07 89.7% 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 Mon Oct 10 2011 at 17:07:53 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3689 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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: 2.508809 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): -30.01000 33.84500 ymin,ymax (A): -31.51900 31.33500 zmin,zma (A): 29.12400 86.44600 x,y,z range (A): 63.85500 62.85400 57.32200 scale (grids/A): 2.508809 object centre (A): 1.917500 -9.2000008E-02 57.78500 number of atom coordinates read : 3689 total number of charged atoms : 3491 net assigned charge : 5.706039 assigned positive charge : 555.3007 centred at (gu) : 89.96126 97.60426 95.50388 assigned negative charge : -549.5964 centred at (gu) : 90.53390 97.69331 95.52830 start vw surface at 0.1800000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 187508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33159 grid for indexing accessible points = 1.400000 m= 85913 mr = 133604 m= 24303 mr = 67319 m= 4200 mr = 17932 m= 380 mr = 2769 m= 4 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 1.330000 number of dielectric boundary points 80507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 27903 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) : 1.672539 object centre at (A) : 1.917500 -9.2000008E-02 57.78500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8162015E-02 0.1091146 midg,1,midg; midg,igrid,midg -0.2778770 4.2644709E-02 1,midg,midg; igrid,midg,midg 0.2928513 1.4894064E-02 gauss-seidel spectral radius is 0.9991990 estimated iterations to convergence 279 setup time was (sec) 1.620000 now iterating at: 17:07:55 rms-change max change #iterations 10.09489 359.6409 at 10iterations 5.802089 133.5724 at 20iterations 3.310274 80.03560 at 30iterations 1.884596 39.28333 at 40iterations 1.072024 21.46285 at 50iterations 0.6074433 14.04303 at 60iterations 0.3428241 7.202494 at 70iterations 0.1936940 4.169345 at 80iterations 0.1094470 2.049538 at 90iterations 6.1698176E-02 1.270184 at 100iterations 3.4718420E-02 0.7555313 at 110iterations 1.9581549E-02 0.3866558 at 120iterations 1.1027126E-02 0.2023621 at 130iterations 6.2140818E-03 0.1306610 at 140iterations 3.5071396E-03 7.6416016E-02 at 150iterations 1.9907306E-03 3.9907455E-02 at 160iterations 1.1355464E-03 2.3559570E-02 at 170iterations 6.5556756E-04 1.3900757E-02 at 180iterations finished qdiffx linear iterations at : 17:08:05 total time elapsed so far: 11.32000 # loops : 180 mean,max change (kT/e) : 6.5556756E-04 1.3900757E-02 energy calculations done at 11.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 17:08:05 11.500u 0.180s 0:12.10 96.5% 0+0k 0+0io 0pf+0w