Sat Oct 15 13:42:47 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 13:42:47 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6325065 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): 3.130000 57.42100 ymin,ymax (A): -4.108000 52.17600 zmin,zma (A): -31.41800 23.34900 x,y,z range (A): 54.29100 56.28400 54.76700 scale (grids/A): 0.6325065 object centre (A): 30.27550 24.03400 -4.034500 number of atom coordinates read : 2820 total number of charged atoms : 2664 net assigned charge : -5.499989 assigned positive charge : 426.9111 centred at (gu) : 90.64036 87.43739 89.84850 assigned negative charge : -432.4122 centred at (gu) : 90.60355 87.30745 89.65965 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7642 nv = 96 ne = 84 npr = 56574 no. pairs analyzed = 56574 no. exposed pairs = 3614 no. arc points = 25757 no. surface atoms = 1207 nbur = 1613 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 4056 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.3200000 number of dielectric boundary points 3942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2633 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9296 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7050001E-08 1.2970098E-08 midg,1,midg; midg,igrid,midg -3.4786979E-08 4.1701744E-09 1,midg,midg; igrid,midg,midg -8.5862268E-09 -2.3892928E-09 gauss-seidel spectral radius is 0.9870778 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 13:42:48 rms-change max change #iterations 0.1442625 20.77658 at 10iterations 1.4167867E-02 1.973627 at 20iterations 1.3922512E-03 0.1877718 at 30iterations 1.4101395E-04 2.2929192E-02 at 40iterations 1.6897307E-05 2.8362274E-03 at 50iterations finished qdiffx linear iterations at : 13:42:51 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 1.6897307E-05 2.8362274E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 13:42:52 4.150u 0.427s 0:04.87 93.8% 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 13:42:52 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 = 2820 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897520 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): 3.130000 57.42100 ymin,ymax (A): -4.108000 52.17600 zmin,zma (A): -31.41800 23.34900 x,y,z range (A): 54.29100 56.28400 54.76700 scale (grids/A): 1.897520 object centre (A): 30.27550 24.03400 -4.034500 number of atom coordinates read : 2820 total number of charged atoms : 2664 net assigned charge : -5.499989 assigned positive charge : 426.9111 centred at (gu) : 91.92020 82.31120 89.54465 assigned negative charge : -432.4122 centred at (gu) : 91.81042 81.92205 88.97881 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25757 grid for indexing accessible points = 1.400000 m= 27976 mr = 55952 m= 4346 mr = 19843 m= 266 mr = 2637 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 3583 time to turn everything in is 0.6300000 number of dielectric boundary points 36342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20966 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) : 0.6325065 object centre at (A) : 30.27550 24.03400 -4.034500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3832158E-02 -4.7981204E-03 midg,1,midg; midg,igrid,midg -5.5795033E-02 2.1990672E-02 1,midg,midg; igrid,midg,midg -4.0225226E-02 -1.4112281E-02 gauss-seidel spectral radius is 0.9986483 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 13:42:53 rms-change max change #iterations 4.484405 186.1199 at 10iterations 2.100698 69.69133 at 20iterations 0.9906880 29.34961 at 30iterations 0.4630638 14.26821 at 40iterations 0.2181635 6.636285 at 50iterations 0.1023057 3.174514 at 60iterations 4.8044473E-02 1.422266 at 70iterations 2.2587992E-02 0.7269878 at 80iterations 1.0595611E-02 0.3592434 at 90iterations 4.9934946E-03 0.1424942 at 100iterations 2.3626559E-03 7.2257996E-02 at 110iterations 1.1153588E-03 3.2978058E-02 at 120iterations finished qdiffx linear iterations at : 13:43:02 total time elapsed so far: 9.990000 # loops : 120 mean,max change (kT/e) : 1.1153588E-03 3.2978058E-02 energy calculations done at 9.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.16000 DelPhi exited at 13:43:03 10.168u 0.502s 0:11.18 95.3% 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 Sat Oct 15 2011 at 13:43:03 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 = 2820 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.846279 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): 3.130000 57.42100 ymin,ymax (A): -4.108000 52.17600 zmin,zma (A): -31.41800 23.34900 x,y,z range (A): 54.29100 56.28400 54.76700 scale (grids/A): 2.846279 object centre (A): 30.27550 24.03400 -4.034500 number of atom coordinates read : 2820 total number of charged atoms : 2664 net assigned charge : -5.499989 assigned positive charge : 426.9111 centred at (gu) : 92.88004 78.46650 89.31672 assigned negative charge : -432.4122 centred at (gu) : 92.71547 77.88294 88.46799 start vw surface at 0.1300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 190500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25757 grid for indexing accessible points = 1.400000 m= 91777 mr = 135958 m= 31552 mr = 73765 m= 7767 mr = 24540 m= 1185 mr = 5733 m= 67 mr = 795 m= 0 mr = 25 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 12493 time to turn everything in is 1.690000 number of dielectric boundary points 82032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 21311 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) : 1.897520 object centre at (A) : 30.27550 24.03400 -4.034500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6886584 -5.5844370E-02 midg,1,midg; midg,igrid,midg -0.6066955 0.2270365 1,midg,midg; igrid,midg,midg -0.4089211 -0.4000182 gauss-seidel spectral radius is 0.9992736 estimated iterations to convergence 293 setup time was (sec) 2.030000 now iterating at: 13:43:06 rms-change max change #iterations 10.70067 432.1606 at 10iterations 6.289983 141.6758 at 20iterations 3.680411 79.61694 at 30iterations 2.142996 45.01563 at 40iterations 1.244555 27.09781 at 50iterations 0.7228473 13.90690 at 60iterations 0.4183740 7.904907 at 70iterations 0.2421097 4.811029 at 80iterations 0.1401413 2.539214 at 90iterations 8.1008606E-02 1.923656 at 100iterations 4.6756361E-02 0.7822781 at 110iterations 2.7072597E-02 0.4865494 at 120iterations 1.5605547E-02 0.2971311 at 130iterations 9.0420591E-03 0.1533203 at 140iterations 5.2278247E-03 9.6157074E-02 at 150iterations 3.0147429E-03 5.1725388E-02 at 160iterations 1.7538649E-03 3.3451080E-02 at 170iterations 1.0190487E-03 1.9634247E-02 at 180iterations finished qdiffx linear iterations at : 13:43:21 total time elapsed so far: 17.30000 # loops : 180 mean,max change (kT/e) : 1.0190487E-03 1.9634247E-02 energy calculations done at 17.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.55000 DelPhi exited at 13:43:22 17.555u 0.502s 0:18.52 97.4% 0+0k 0+0io 0pf+0w