Mon Oct 10 14:13:52 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 14:13:52 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5676 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 541 has a net charge of 0.5140 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 718 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.4962364 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): 26.09900 88.39900 ymin,ymax (A): -84.15600 -12.41600 zmin,zma (A): -36.57900 31.36000 x,y,z range (A): 62.30000 71.74000 67.93900 scale (grids/A): 0.4962364 object centre (A): 57.24900 -48.28600 -2.609501 number of atom coordinates read : 5676 total number of charged atoms : 5504 net assigned charge : -2.371957 assigned positive charge : 876.6542 centred at (gu) : 91.13650 90.29189 90.19702 assigned negative charge : -879.0339 centred at (gu) : 91.06473 90.32153 90.13657 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8691 nv = 96 ne = 84 npr = 114115 no. pairs analyzed = 114115 no. exposed pairs = 7021 no. arc points = 48163 no. surface atoms = 2350 nbur = 3326 mkacc time = 0.2400000 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 = 1.708000 m= 307 mr = 4572 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4583 ## 710 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11770 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1596594E-10 8.7362950E-11 midg,1,midg; midg,igrid,midg 2.8648604E-11 -7.5203822E-11 1,midg,midg; igrid,midg,midg -1.0424115E-10 1.3940497E-10 gauss-seidel spectral radius is 0.9792975 estimated iterations to convergence 58 setup time was (sec) 0.7900000 now iterating at: 14:13:53 rms-change max change #iterations 6.5754101E-02 10.10876 at 10iterations 4.9119876E-03 0.7734337 at 20iterations 1.4696437E-03 0.3177357 at 30iterations 6.0028851E-04 0.1371555 at 40iterations 2.5000566E-04 5.8538437E-02 at 50iterations finished qdiffx linear iterations at : 14:13:55 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.5000566E-04 5.8538437E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 14:13:56 3.554u 0.214s 0:04.22 89.0% 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 14:13:56 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5676 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 541 has a net charge of 0.5140 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 718 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: 1.488709 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): 26.09900 88.39900 ymin,ymax (A): -84.15600 -12.41600 zmin,zma (A): -36.57900 31.36000 x,y,z range (A): 62.30000 71.74000 67.93900 scale (grids/A): 1.488709 object centre (A): 57.24900 -48.28600 -2.609501 number of atom coordinates read : 5676 total number of charged atoms : 5504 net assigned charge : -2.371957 assigned positive charge : 876.6542 centred at (gu) : 93.40755 90.87398 90.58868 assigned negative charge : -879.0339 centred at (gu) : 93.19411 90.96420 90.40969 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 99900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48163 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 29022 mr = 69341 m= 2382 mr = 19494 m= 53 mr = 965 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1561 time to turn everything in is 0.6800000 number of dielectric boundary points 41555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 627 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 40943 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) : 0.4962364 object centre at (A) : 57.24900 -48.28600 -2.609501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4874273E-03 -3.8462153E-03 midg,1,midg; midg,igrid,midg -1.3521601E-02 -9.3860375E-03 1,midg,midg; igrid,midg,midg -7.6885242E-03 1.1441047E-02 gauss-seidel spectral radius is 0.9980664 estimated iterations to convergence 181 setup time was (sec) 0.9800000 now iterating at: 14:13:57 rms-change max change #iterations 3.995750 150.9988 at 10iterations 1.619795 52.92573 at 20iterations 0.6585588 20.13890 at 30iterations 0.2668359 8.518299 at 40iterations 0.1085528 3.554405 at 50iterations 4.4355959E-02 1.338766 at 60iterations 1.8337784E-02 0.5493851 at 70iterations 7.7721891E-03 0.2603264 at 80iterations 3.5542918E-03 0.1426430 at 90iterations 1.8497108E-03 7.3986053E-02 at 100iterations 1.1240357E-03 5.0346375E-02 at 110iterations 7.6133030E-04 3.5682678E-02 at 120iterations finished qdiffx linear iterations at : 14:14:04 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 7.6133030E-04 3.5682678E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 14:14:04 7.694u 0.218s 0:08.31 95.0% 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 14:14:04 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5676 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 541 has a net charge of 0.5140 !!! WARNING: HIZ 655 has a net charge of 0.2000 !!! WARNING: ZN7 718 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.233064 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): 26.09900 88.39900 ymin,ymax (A): -84.15600 -12.41600 zmin,zma (A): -36.57900 31.36000 x,y,z range (A): 62.30000 71.74000 67.93900 scale (grids/A): 2.233064 object centre (A): 57.24900 -48.28600 -2.609501 number of atom coordinates read : 5676 total number of charged atoms : 5504 net assigned charge : -2.371957 assigned positive charge : 876.6542 centred at (gu) : 95.11058 91.31061 90.88273 assigned negative charge : -879.0339 centred at (gu) : 94.79099 91.44626 90.61442 start vw surface at 0.2100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 232669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48163 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 104826 mr = 170332 m= 26091 mr = 82056 m= 3330 mr = 19012 m= 149 mr = 1911 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 5125 time to turn everything in is 1.630000 number of dielectric boundary points 93731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 43870 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) : 1.488709 object centre at (A) : 57.24900 -48.28600 -2.609501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2698752 -0.1283524 midg,1,midg; midg,igrid,midg -0.4248696 -0.1968567 1,midg,midg; igrid,midg,midg -0.1159286 0.2624178 gauss-seidel spectral radius is 0.9991660 estimated iterations to convergence 273 setup time was (sec) 1.950000 now iterating at: 14:14:07 rms-change max change #iterations 11.05864 273.9457 at 10iterations 6.323902 145.6145 at 20iterations 3.604040 78.00289 at 30iterations 2.037945 44.97414 at 40iterations 1.151430 23.47432 at 50iterations 0.6470458 13.76636 at 60iterations 0.3628757 6.947540 at 70iterations 0.2033971 3.469250 at 80iterations 0.1134885 2.236904 at 90iterations 6.3269079E-02 1.201008 at 100iterations 3.5416421E-02 0.6895466 at 110iterations 1.9776018E-02 0.3643818 at 120iterations 1.1095047E-02 0.2149487 at 130iterations 6.2418953E-03 0.1240883 at 140iterations 3.5628949E-03 7.3930979E-02 at 150iterations 2.0707527E-03 4.3968201E-02 at 160iterations 1.2573809E-03 2.9109955E-02 at 170iterations 8.0828648E-04 2.2384644E-02 at 180iterations finished qdiffx linear iterations at : 14:14:18 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 8.0828648E-04 2.2384644E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 14:14:19 13.765u 0.236s 0:14.43 96.9% 0+0k 0+0io 0pf+0w