Sat Oct 15 15:28:42 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 15 2011 at 15:28:42 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4781 !!! WARNING: HIR 202 has a net charge of 0.5140 !!! WARNING: SEP 364 has a net charge of -0.4750 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: 0.5098752 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): 35.99700 105.8180 ymin,ymax (A): 5.653000 65.66800 zmin,zma (A): -13.01700 47.33500 x,y,z range (A): 69.82100 60.01500 60.35201 scale (grids/A): 0.5098752 object centre (A): 70.90750 35.66050 17.15900 number of atom coordinates read : 4781 total number of charged atoms : 4609 net assigned charge : -6.960961 assigned positive charge : 752.4954 centred at (gu) : 90.56850 88.95560 89.33685 assigned negative charge : -759.4608 centred at (gu) : 90.68999 89.13273 89.41586 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7749 nv = 96 ne = 84 npr = 93762 no. pairs analyzed = 93762 no. exposed pairs = 6538 no. arc points = 44901 no. surface atoms = 2177 nbur = 2604 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 = 1.680000 m= 264 mr = 3692 m= 2 mr = 3 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 0.3100000 number of dielectric boundary points 4320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4404 ## 654 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3120048E-10 -2.6291927E-10 midg,1,midg; midg,igrid,midg 4.8155419E-10 -4.4323206E-10 1,midg,midg; igrid,midg,midg 1.8805643E-10 -4.9997345E-10 gauss-seidel spectral radius is 0.9803289 estimated iterations to convergence 59 setup time was (sec) 0.4900000 now iterating at: 15:28:43 rms-change max change #iterations 7.1554452E-02 10.68698 at 10iterations 4.2044795E-03 0.6171093 at 20iterations 4.9168844E-04 7.0134163E-02 at 30iterations 1.3968635E-04 1.7153740E-02 at 40iterations 4.6399062E-05 5.3930283E-03 at 50iterations finished qdiffx linear iterations at : 15:28:46 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 4.6399062E-05 5.3930283E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 15:28:46 3.508u 0.182s 0:04.08 90.1% 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 15 2011 at 15:28:47 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4781 !!! WARNING: HIR 202 has a net charge of 0.5140 !!! WARNING: SEP 364 has a net charge of -0.4750 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: 1.529626 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): 35.99700 105.8180 ymin,ymax (A): 5.653000 65.66800 zmin,zma (A): -13.01700 47.33500 x,y,z range (A): 69.82100 60.01500 60.35201 scale (grids/A): 1.529626 object centre (A): 70.90750 35.66050 17.15900 number of atom coordinates read : 4781 total number of charged atoms : 4609 net assigned charge : -6.960961 assigned positive charge : 752.4954 centred at (gu) : 91.70425 86.86565 88.00924 assigned negative charge : -759.4608 centred at (gu) : 92.06947 87.39777 88.24738 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 85136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44901 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25068 mr = 55197 m= 2175 mr = 16175 m= 54 mr = 887 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 40174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 589 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 34591 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) : 0.5098752 object centre at (A) : 70.90750 35.66050 17.15900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7297105E-03 -4.7621103E-03 midg,1,midg; midg,igrid,midg 2.0960623E-03 -9.6710222E-03 1,midg,midg; igrid,midg,midg -8.5593583E-03 -3.6676634E-02 gauss-seidel spectral radius is 0.9981065 estimated iterations to convergence 183 setup time was (sec) 0.6300000 now iterating at: 15:28:47 rms-change max change #iterations 3.942650 161.5759 at 10iterations 1.597146 56.52007 at 20iterations 0.6528178 21.09274 at 30iterations 0.2670135 9.172806 at 40iterations 0.1091614 4.396512 at 50iterations 4.4649549E-02 1.520294 at 60iterations 1.8307226E-02 0.5510406 at 70iterations 7.4999933E-03 0.2824554 at 80iterations 3.0967558E-03 9.1293335E-02 at 90iterations 1.2924125E-03 4.0836334E-02 at 100iterations 5.5775139E-04 1.9323349E-02 at 110iterations 2.5359192E-04 7.7800751E-03 at 120iterations finished qdiffx linear iterations at : 15:28:55 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 2.5359192E-04 7.7800751E-03 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 15:28:55 7.991u 0.245s 0:08.62 95.4% 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 Sat Oct 15 2011 at 15:28:55 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4781 !!! WARNING: HIR 202 has a net charge of 0.5140 !!! WARNING: SEP 364 has a net charge of -0.4750 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: 2.294439 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): 35.99700 105.8180 ymin,ymax (A): 5.653000 65.66800 zmin,zma (A): -13.01700 47.33500 x,y,z range (A): 69.82100 60.01500 60.35201 scale (grids/A): 2.294439 object centre (A): 70.90750 35.66050 17.15900 number of atom coordinates read : 4781 total number of charged atoms : 4609 net assigned charge : -6.960961 assigned positive charge : 752.4954 centred at (gu) : 92.55582 85.29818 87.01346 assigned negative charge : -759.4608 centred at (gu) : 93.10406 86.09654 87.37101 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 198205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44901 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 87262 mr = 136825 m= 23343 mr = 66025 m= 3125 mr = 16744 m= 142 mr = 1820 m= 4 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 90644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 36760 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) : 1.529626 object centre at (A) : 70.90750 35.66050 17.15900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6692987E-02 -0.1188633 midg,1,midg; midg,igrid,midg -6.7952260E-02 -0.1070514 1,midg,midg; igrid,midg,midg -0.2838374 -1.050430 gauss-seidel spectral radius is 0.9991649 estimated iterations to convergence 273 setup time was (sec) 1.270000 now iterating at: 15:28:57 rms-change max change #iterations 10.80216 318.1174 at 10iterations 6.266053 163.3526 at 20iterations 3.594837 76.14761 at 30iterations 2.055558 43.88710 at 40iterations 1.165786 23.01643 at 50iterations 0.6581165 13.56783 at 60iterations 0.3709814 8.107090 at 70iterations 0.2085003 4.117777 at 80iterations 0.1170127 2.387037 at 90iterations 6.5498710E-02 1.393063 at 100iterations 3.6578126E-02 0.6892052 at 110iterations 2.0429133E-02 0.3889961 at 120iterations 1.1410588E-02 0.2198715 at 130iterations 6.3667302E-03 0.1362915 at 140iterations 3.5577840E-03 8.0726624E-02 at 150iterations 1.9799692E-03 3.7326813E-02 at 160iterations 1.1031012E-03 2.0530701E-02 at 170iterations 6.1705417E-04 1.1573792E-02 at 180iterations finished qdiffx linear iterations at : 15:29:08 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 6.1705417E-04 1.1573792E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 15:29:09 12.863u 0.201s 0:13.37 97.6% 0+0k 0+0io 0pf+0w