Sat Oct 15 15:30:39 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 15:30:39 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2315 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG7 705 has a net charge of 1.4000 !!! WARNING: ZN7 706 has a net charge of 1.4000 !!! WARNING: ZN7 707 has a net charge of 1.4000 !!! WARNING: ZN7 708 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: 0.6897087 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): 15.62900 62.95200 ymin,ymax (A): -3.571000 33.50500 zmin,zma (A): 20.11000 71.72600 x,y,z range (A): 47.32300 37.07600 51.61600 scale (grids/A): 0.6897087 object centre (A): 39.29050 14.96700 45.91800 number of atom coordinates read : 2315 total number of charged atoms : 1990 net assigned charge : 11.32501 assigned positive charge : 328.6739 centred at (gu) : 91.49080 89.77924 89.19601 assigned negative charge : -317.3491 centred at (gu) : 91.57160 89.71577 89.09015 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6736 nv = 96 ne = 84 npr = 43099 no. pairs analyzed = 43099 no. exposed pairs = 2534 no. arc points = 17250 no. surface atoms = 867 nbur = 1448 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 3896 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1687 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7685 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1275388E-08 8.3616101E-08 midg,1,midg; midg,igrid,midg 4.3275737E-08 8.0402813E-08 1,midg,midg; igrid,midg,midg 6.7108175E-08 4.6970214E-08 gauss-seidel spectral radius is 0.9890487 estimated iterations to convergence 78 setup time was (sec) 0.3400000 now iterating at: 15:30:40 rms-change max change #iterations 0.1919899 26.34159 at 10iterations 2.2630589E-02 3.108473 at 20iterations 2.6530765E-03 0.3423233 at 30iterations 3.1605287E-04 4.0361404E-02 at 40iterations 3.9468418E-05 6.2894821E-03 at 50iterations finished qdiffx linear iterations at : 15:30:43 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.9468418E-05 6.2894821E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 15:30:43 3.326u 0.183s 0:04.03 86.8% 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 Sat Oct 15 2011 at 15:30:43 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2315 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG7 705 has a net charge of 1.4000 !!! WARNING: ZN7 706 has a net charge of 1.4000 !!! WARNING: ZN7 707 has a net charge of 1.4000 !!! WARNING: ZN7 708 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: 2.069126 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): 15.62900 62.95200 ymin,ymax (A): -3.571000 33.50500 zmin,zma (A): 20.11000 71.72600 x,y,z range (A): 47.32300 37.07600 51.61600 scale (grids/A): 2.069126 object centre (A): 39.29050 14.96700 45.91800 number of atom coordinates read : 2315 total number of charged atoms : 1990 net assigned charge : 11.32501 assigned positive charge : 328.6739 centred at (gu) : 94.47225 89.33778 87.58793 assigned negative charge : -317.3491 centred at (gu) : 94.71495 89.14725 87.27054 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17250 grid for indexing accessible points = 1.400000 m= 28604 mr = 51225 m= 5371 mr = 21799 m= 438 mr = 3552 m= 7 mr = 215 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 302 time to turn everything in is 0.3800000 number of dielectric boundary points 29521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 15790 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) : 0.6897087 object centre at (A) : 39.29050 14.96700 45.91800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6841264E-02 5.5707935E-02 midg,1,midg; midg,igrid,midg 2.7313134E-02 4.6660379E-02 1,midg,midg; igrid,midg,midg 2.6643995E-02 3.6574122E-02 gauss-seidel spectral radius is 0.9987782 estimated iterations to convergence 227 setup time was (sec) 0.5900000 now iterating at: 15:30:44 rms-change max change #iterations 4.463740 179.3869 at 10iterations 2.193652 77.64073 at 20iterations 1.062526 34.09351 at 30iterations 0.5206937 18.35933 at 40iterations 0.2536041 7.922527 at 50iterations 0.1237195 3.599380 at 60iterations 6.0514338E-02 1.752560 at 70iterations 2.9615546E-02 0.8958483 at 80iterations 1.4469068E-02 0.4135208 at 90iterations 7.0934817E-03 0.2373762 at 100iterations 3.4493385E-03 0.1203079 at 110iterations 1.6935886E-03 6.3125730E-02 at 120iterations finished qdiffx linear iterations at : 15:30:51 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.6935886E-03 6.3125730E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 15:30:52 7.752u 0.171s 0:08.32 95.1% 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 15:30:52 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2315 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG7 705 has a net charge of 1.4000 !!! WARNING: ZN7 706 has a net charge of 1.4000 !!! WARNING: ZN7 707 has a net charge of 1.4000 !!! WARNING: ZN7 708 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: 3.103689 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): 15.62900 62.95200 ymin,ymax (A): -3.571000 33.50500 zmin,zma (A): 20.11000 71.72600 x,y,z range (A): 47.32300 37.07600 51.61600 scale (grids/A): 3.103689 object centre (A): 39.29050 14.96700 45.91800 number of atom coordinates read : 2315 total number of charged atoms : 1990 net assigned charge : 11.32501 assigned positive charge : 328.6739 centred at (gu) : 96.70831 89.00672 86.38179 assigned negative charge : -317.3491 centred at (gu) : 97.07236 88.72089 85.90582 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 165625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17250 grid for indexing accessible points = 1.400000 m= 89932 mr = 123170 m= 36066 mr = 74934 m= 10018 mr = 29757 m= 1864 mr = 7745 m= 160 mr = 1393 m= 3 mr = 82 m= 0 mr = 2 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1034 time to turn everything in is 1.090000 number of dielectric boundary points 66585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 15920 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) : 2.069126 object centre at (A) : 39.29050 14.96700 45.91800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4033914 0.4092760 midg,1,midg; midg,igrid,midg 0.2423367 0.4036368 1,midg,midg; igrid,midg,midg 0.2143985 0.5604756 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 1.320000 now iterating at: 15:30:53 rms-change max change #iterations 10.14920 416.7887 at 10iterations 5.959891 134.5729 at 20iterations 3.497829 78.59936 at 30iterations 2.050332 48.06660 at 40iterations 1.199283 24.48053 at 50iterations 0.7001451 12.21621 at 60iterations 0.4082697 7.862619 at 70iterations 0.2379576 4.427006 at 80iterations 0.1389731 2.504047 at 90iterations 8.0926232E-02 1.697361 at 100iterations 4.7126450E-02 0.9659309 at 110iterations 2.7431656E-02 0.5433102 at 120iterations 1.5947266E-02 0.2820644 at 130iterations 9.3242256E-03 0.1799393 at 140iterations 5.4696193E-03 0.1033983 at 150iterations 3.2172881E-03 6.4641953E-02 at 160iterations 1.9099577E-03 3.7628174E-02 at 170iterations 1.1593327E-03 2.3750305E-02 at 180iterations finished qdiffx linear iterations at : 15:31:04 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 1.1593327E-03 2.3750305E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 15:31:05 12.596u 0.215s 0:13.11 97.6% 0+0k 0+0io 0pf+0w