Tue Oct 11 05:28:20 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 Tue Oct 11 2011 at 05:28:20 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7343840 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): -6.243000 40.36000 ymin,ymax (A): 11.95000 60.42600 zmin,zma (A): 3.909000 46.47000 x,y,z range (A): 46.60300 48.47600 42.56100 scale (grids/A): 0.7343840 object centre (A): 17.05850 36.18800 25.18950 number of atom coordinates read : 2049 total number of charged atoms : 1915 net assigned charge : 6.931010 assigned positive charge : 310.1871 centred at (gu) : 89.15692 91.04080 90.09248 assigned negative charge : -303.2562 centred at (gu) : 89.27674 90.89988 90.17137 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7641 nv = 96 ne = 84 npr = 41306 no. pairs analyzed = 41306 no. exposed pairs = 2534 no. arc points = 17187 no. surface atoms = 867 nbur = 1182 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 4435 m= 5 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1490 ## 124 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6994716E-07 3.8234464E-08 midg,1,midg; midg,igrid,midg -1.2497780E-08 2.7374756E-07 1,midg,midg; igrid,midg,midg 2.4290114E-07 2.5691929E-09 gauss-seidel spectral radius is 0.9903257 estimated iterations to convergence 83 setup time was (sec) 0.5300000 now iterating at: 05:28:21 rms-change max change #iterations 0.2365347 32.76279 at 10iterations 3.2050401E-02 4.895821 at 20iterations 4.6247416E-03 0.5637856 at 30iterations 8.7033468E-04 9.9525452E-02 at 40iterations 2.4023243E-04 2.5669098E-02 at 50iterations finished qdiffx linear iterations at : 05:28:25 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 2.4023243E-04 2.5669098E-02 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 05:28:25 4.366u 0.403s 0:05.20 91.5% 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 Tue Oct 11 2011 at 05:28:25 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.203152 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): -6.243000 40.36000 ymin,ymax (A): 11.95000 60.42600 zmin,zma (A): 3.909000 46.47000 x,y,z range (A): 46.60300 48.47600 42.56100 scale (grids/A): 2.203152 object centre (A): 17.05850 36.18800 25.18950 number of atom coordinates read : 2049 total number of charged atoms : 1915 net assigned charge : 6.931010 assigned positive charge : 310.1871 centred at (gu) : 87.47131 93.12278 90.27767 assigned negative charge : -303.2562 centred at (gu) : 87.83038 92.69962 90.51414 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17187 grid for indexing accessible points = 1.400000 m= 34043 mr = 57026 m= 7121 mr = 26205 m= 715 mr = 4897 m= 26 mr = 354 m= 0 mr = 6 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 33329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15238 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) : 0.7343840 object centre at (A) : 17.05850 36.18800 25.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1469729E-02 2.5018524E-02 midg,1,midg; midg,igrid,midg 3.5200983E-02 0.1166165 1,midg,midg; igrid,midg,midg 4.3654479E-02 -5.1403534E-02 gauss-seidel spectral radius is 0.9989004 estimated iterations to convergence 239 setup time was (sec) 0.9600000 now iterating at: 05:28:27 rms-change max change #iterations 4.850510 212.8517 at 10iterations 2.448661 82.68652 at 20iterations 1.244146 43.02775 at 30iterations 0.6304974 19.33017 at 40iterations 0.3204805 9.247247 at 50iterations 0.1629305 4.798859 at 60iterations 8.2518242E-02 2.420162 at 70iterations 4.2143367E-02 1.176601 at 80iterations 2.1580828E-02 0.6007576 at 90iterations 1.1081331E-02 0.3015900 at 100iterations 5.7676886E-03 0.1639099 at 110iterations 3.0880875E-03 9.3658447E-02 at 120iterations finished qdiffx linear iterations at : 05:28:36 total time elapsed so far: 10.44000 # loops : 120 mean,max change (kT/e) : 3.0880875E-03 9.3658447E-02 energy calculations done at 10.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 05:28:37 10.598u 0.476s 0:11.36 97.3% 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 Tue Oct 11 2011 at 05:28:37 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.304728 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): -6.243000 40.36000 ymin,ymax (A): 11.95000 60.42600 zmin,zma (A): 3.909000 46.47000 x,y,z range (A): 46.60300 48.47600 42.56100 scale (grids/A): 3.304728 object centre (A): 17.05850 36.18800 25.18950 number of atom coordinates read : 2049 total number of charged atoms : 1915 net assigned charge : 6.931010 assigned positive charge : 310.1871 centred at (gu) : 86.20686 94.68404 90.41646 assigned negative charge : -303.2562 centred at (gu) : 86.74562 94.04951 90.77126 start vw surface at 0.1000000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 183656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17187 grid for indexing accessible points = 1.400000 m= 103681 mr = 136665 m= 45141 mr = 86788 m= 13727 mr = 37580 m= 2908 mr = 10835 m= 354 mr = 2134 m= 23 mr = 215 m= 0 mr = 9 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.220000 number of dielectric boundary points 75264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 15319 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) : 2.203152 object centre at (A) : 17.05850 36.18800 25.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1359176 0.2141702 midg,1,midg; midg,igrid,midg 0.2527472 0.8751695 1,midg,midg; igrid,midg,midg 0.3723210 -0.5907719 gauss-seidel spectral radius is 0.9993151 estimated iterations to convergence 301 setup time was (sec) 2.540000 now iterating at: 05:28:40 rms-change max change #iterations 10.60848 313.3622 at 10iterations 6.331414 157.8930 at 20iterations 3.774963 69.04983 at 30iterations 2.243169 42.02065 at 40iterations 1.332730 27.89867 at 50iterations 0.7876973 15.02018 at 60iterations 0.4668905 7.712379 at 70iterations 0.2761770 4.891829 at 80iterations 0.1630797 2.952637 at 90iterations 9.6747227E-02 1.592516 at 100iterations 5.7235219E-02 0.9664497 at 110iterations 3.4214932E-02 0.6125031 at 120iterations 2.0590290E-02 0.3406258 at 130iterations 1.2682765E-02 0.2379990 at 140iterations 8.0798389E-03 0.1473885 at 150iterations 5.4180929E-03 9.8556519E-02 at 160iterations 3.8586194E-03 6.9705963E-02 at 170iterations 2.9236276E-03 4.9530029E-02 at 180iterations finished qdiffx linear iterations at : 05:28:56 total time elapsed so far: 18.73000 # loops : 180 mean,max change (kT/e) : 2.9236276E-03 4.9530029E-02 energy calculations done at 18.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.90000 DelPhi exited at 05:28:57 18.900u 0.495s 0:20.00 96.9% 0+0k 0+0io 0pf+0w