Mon Oct 10 14:24:28 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 14:24:28 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6277109 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): -7.655000 44.38800 ymin,ymax (A): 3.938000 60.65200 zmin,zma (A): -14.43700 36.90100 x,y,z range (A): 52.04300 56.71400 51.33800 scale (grids/A): 0.6277109 object centre (A): 18.36650 32.29500 11.23200 number of atom coordinates read : 2399 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 352.0482 centred at (gu) : 89.84174 89.36189 89.94891 assigned negative charge : -356.0485 centred at (gu) : 89.60591 89.42388 89.94717 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6400 nv = 96 ne = 84 npr = 48422 no. pairs analyzed = 48422 no. exposed pairs = 3177 no. arc points = 22424 no. surface atoms = 1073 nbur = 1326 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3323 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2194 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7675 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2185855E-09 -3.8671106E-09 midg,1,midg; midg,igrid,midg 7.7718043E-10 -7.6593549E-09 1,midg,midg; igrid,midg,midg -2.3259943E-08 1.2969545E-08 gauss-seidel spectral radius is 0.9868438 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 14:24:29 rms-change max change #iterations 0.1267915 18.47396 at 10iterations 1.2033942E-02 1.703552 at 20iterations 1.1261778E-03 0.1560946 at 30iterations 1.0654180E-04 1.6289234E-02 at 40iterations 1.0174009E-05 1.5754700E-03 at 50iterations finished qdiffx linear iterations at : 14:24:32 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.0174009E-05 1.5754700E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 14:24:32 3.520u 0.194s 0:04.05 91.6% 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 14:24:33 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 1.883133 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): -7.655000 44.38800 ymin,ymax (A): 3.938000 60.65200 zmin,zma (A): -14.43700 36.90100 x,y,z range (A): 52.04300 56.71400 51.33800 scale (grids/A): 1.883133 object centre (A): 18.36650 32.29500 11.23200 number of atom coordinates read : 2399 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 352.0482 centred at (gu) : 89.52484 88.08504 89.84617 assigned negative charge : -356.0485 centred at (gu) : 88.81730 88.27142 89.84126 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22424 grid for indexing accessible points = 1.400000 m= 23267 mr = 46745 m= 3114 mr = 16276 m= 150 mr = 1561 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.5400000 number of dielectric boundary points 31304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17637 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) : 0.6277109 object centre at (A) : 18.36650 32.29500 11.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8802568E-04 -1.7027672E-02 midg,1,midg; midg,igrid,midg 5.8126827E-03 -3.4781112E-03 1,midg,midg; igrid,midg,midg -4.0657576E-02 8.2851863E-03 gauss-seidel spectral radius is 0.9985906 estimated iterations to convergence 211 setup time was (sec) 0.8200000 now iterating at: 14:24:34 rms-change max change #iterations 3.935944 194.8069 at 10iterations 1.821092 62.73196 at 20iterations 0.8390707 30.53816 at 30iterations 0.3873967 12.87683 at 40iterations 0.1793581 6.758954 at 50iterations 8.3033592E-02 2.830063 at 60iterations 3.8333777E-02 1.311496 at 70iterations 1.7614497E-02 0.5588684 at 80iterations 8.1715407E-03 0.3100815 at 90iterations 3.7828702E-03 0.1285267 at 100iterations 1.7480002E-03 5.8696747E-02 at 110iterations 8.0892723E-04 3.1950951E-02 at 120iterations finished qdiffx linear iterations at : 14:24:40 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 8.0892723E-04 3.1950951E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 14:24:41 7.876u 0.231s 0:08.45 95.8% 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 Mon Oct 10 2011 at 14:24:41 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 2.824699 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): -7.655000 44.38800 ymin,ymax (A): 3.938000 60.65200 zmin,zma (A): -14.43700 36.90100 x,y,z range (A): 52.04300 56.71400 51.33800 scale (grids/A): 2.824699 object centre (A): 18.36650 32.29500 11.23200 number of atom coordinates read : 2399 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 352.0482 centred at (gu) : 89.28713 87.12751 89.76926 assigned negative charge : -356.0485 centred at (gu) : 88.22585 87.40697 89.76187 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 160855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22424 grid for indexing accessible points = 1.400000 m= 77181 mr = 114165 m= 25298 mr = 61533 m= 5200 mr = 19129 m= 603 mr = 3366 m= 35 mr = 314 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 746 time to turn everything in is 1.340000 number of dielectric boundary points 70654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 17923 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) : 1.883133 object centre at (A) : 18.36650 32.29500 11.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9362002E-02 -0.2833099 midg,1,midg; midg,igrid,midg -3.9869593E-03 5.2597001E-03 1,midg,midg; igrid,midg,midg -0.4209104 3.7382152E-02 gauss-seidel spectral radius is 0.9992483 estimated iterations to convergence 288 setup time was (sec) 1.660000 now iterating at: 14:24:43 rms-change max change #iterations 9.481941 335.2213 at 10iterations 5.568438 132.4211 at 20iterations 3.252473 76.95659 at 30iterations 1.887256 39.16088 at 40iterations 1.091418 26.56768 at 50iterations 0.6301278 13.15580 at 60iterations 0.3629818 8.174124 at 70iterations 0.2089453 4.414879 at 80iterations 0.1197884 3.232848 at 90iterations 6.8760894E-02 1.408176 at 100iterations 3.9350130E-02 0.7845421 at 110iterations 2.2560963E-02 0.4547729 at 120iterations 1.2933954E-02 0.2785501 at 130iterations 7.4047311E-03 0.1532955 at 140iterations 4.2420160E-03 8.2569614E-02 at 150iterations 2.4230245E-03 4.8276901E-02 at 160iterations 1.3890561E-03 2.6588440E-02 at 170iterations 7.9437223E-04 1.5012741E-02 at 180iterations finished qdiffx linear iterations at : 14:24:55 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 7.9437223E-04 1.5012741E-02 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.52000 DelPhi exited at 14:24:55 13.517u 0.241s 0:14.32 96.0% 0+0k 0+0io 0pf+0w