Sun Oct 9 16:00:00 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+sph.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 = amb.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 Sun Oct 9 2011 at 16:00:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6361119 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): -15.20100 37.06100 ymin,ymax (A): 3.634000 56.21900 zmin,zma (A): -34.56200 21.40300 x,y,z range (A): 52.26200 52.58500 55.96500 scale (grids/A): 0.6361119 object centre (A): 10.93000 29.92650 -6.579500 number of atom coordinates read : 3038 total number of charged atoms : 2894 net assigned charge : -5.499987 assigned positive charge : 447.9792 centred at (gu) : 90.50739 91.17995 88.71636 assigned negative charge : -453.4806 centred at (gu) : 90.53584 91.31500 88.66397 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8213 nv = 96 ne = 84 npr = 62696 no. pairs analyzed = 62696 no. exposed pairs = 3726 no. arc points = 26145 no. surface atoms = 1259 nbur = 1779 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4536 m= 5 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2518 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9944 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7417772E-08 -4.0722317E-10 midg,1,midg; midg,igrid,midg 7.2351893E-09 -3.0403989E-08 1,midg,midg; igrid,midg,midg -3.0161145E-09 -1.1437976E-08 gauss-seidel spectral radius is 0.9872361 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 16:00:01 rms-change max change #iterations 0.1556305 23.15498 at 10iterations 1.5315970E-02 1.931366 at 20iterations 1.6105807E-03 0.2316055 at 30iterations 2.9771478E-04 5.5144787E-02 at 40iterations 1.0134808E-04 2.0272255E-02 at 50iterations finished qdiffx linear iterations at : 16:00:04 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.0134808E-04 2.0272255E-02 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 16:00:04 3.167u 0.136s 0:03.58 91.8% 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 Sun Oct 9 2011 at 16:00:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 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: 1.908336 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): -15.20100 37.06100 ymin,ymax (A): 3.634000 56.21900 zmin,zma (A): -34.56200 21.40300 x,y,z range (A): 52.26200 52.58500 55.96500 scale (grids/A): 1.908336 object centre (A): 10.93000 29.92650 -6.579500 number of atom coordinates read : 3038 total number of charged atoms : 2894 net assigned charge : -5.499987 assigned positive charge : 447.9792 centred at (gu) : 91.52136 93.53880 86.14840 assigned negative charge : -453.4806 centred at (gu) : 91.60752 93.94490 85.99181 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 32402 mr = 62094 m= 5554 mr = 23756 m= 324 mr = 3561 m= 4 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 37441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22782 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) : 0.6361119 object centre at (A) : 10.93000 29.92650 -6.579500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0025692E-02 2.5299672E-02 midg,1,midg; midg,igrid,midg -1.9161638E-02 -4.4509191E-02 1,midg,midg; igrid,midg,midg -1.6485251E-02 -3.7893429E-02 gauss-seidel spectral radius is 0.9986787 estimated iterations to convergence 218 setup time was (sec) 0.8800000 now iterating at: 16:00:05 rms-change max change #iterations 4.641600 192.4595 at 10iterations 2.198403 70.45641 at 20iterations 1.041081 31.11947 at 30iterations 0.4943055 14.52538 at 40iterations 0.2340311 6.543777 at 50iterations 0.1113157 3.180694 at 60iterations 5.2710079E-02 1.615816 at 70iterations 2.4981204E-02 0.7091293 at 80iterations 1.1886743E-02 0.3119717 at 90iterations 5.6670359E-03 0.1604843 at 100iterations 2.7375543E-03 7.7430725E-02 at 110iterations 1.3423226E-03 4.1992188E-02 at 120iterations finished qdiffx linear iterations at : 16:00:11 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 1.3423226E-03 4.1992188E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 16:00:12 7.053u 0.146s 0:07.50 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 Sun Oct 9 2011 at 16:00:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 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: 2.862503 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): -15.20100 37.06100 ymin,ymax (A): 3.634000 56.21900 zmin,zma (A): -34.56200 21.40300 x,y,z range (A): 52.26200 52.58500 55.96500 scale (grids/A): 2.862503 object centre (A): 10.93000 29.92650 -6.579500 number of atom coordinates read : 3038 total number of charged atoms : 2894 net assigned charge : -5.499987 assigned positive charge : 447.9792 centred at (gu) : 92.28177 95.30815 84.22249 assigned negative charge : -453.4806 centred at (gu) : 92.41116 95.91732 83.98757 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 205416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 104051 mr = 150577 m= 38881 mr = 84974 m= 10040 mr = 31197 m= 1451 mr = 7548 m= 65 mr = 968 m= 0 mr = 25 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 84615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 23151 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) : 1.908336 object centre at (A) : 10.93000 29.92650 -6.579500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2031524 0.6910386 midg,1,midg; midg,igrid,midg -0.3298607 -0.4420207 1,midg,midg; igrid,midg,midg -0.2659001 -0.3900192 gauss-seidel spectral radius is 0.9992805 estimated iterations to convergence 294 setup time was (sec) 1.800000 now iterating at: 16:00:14 rms-change max change #iterations 10.91465 374.2993 at 10iterations 6.466274 127.1935 at 20iterations 3.790206 69.62183 at 30iterations 2.223129 43.22974 at 40iterations 1.300749 26.91378 at 50iterations 0.7613540 15.34590 at 60iterations 0.4429431 7.784687 at 70iterations 0.2580317 4.745804 at 80iterations 0.1501132 2.643854 at 90iterations 8.7202020E-02 1.504202 at 100iterations 5.0695971E-02 0.9172363 at 110iterations 2.9505314E-02 0.4871941 at 120iterations 1.7129460E-02 0.2939682 at 130iterations 9.9988170E-03 0.1931181 at 140iterations 5.8559659E-03 0.1095781 at 150iterations 3.4589521E-03 7.6265335E-02 at 160iterations 2.0931410E-03 4.1138649E-02 at 170iterations 1.3058286E-03 2.8399467E-02 at 180iterations finished qdiffx linear iterations at : 16:00:23 total time elapsed so far: 11.39000 # loops : 180 mean,max change (kT/e) : 1.3058286E-03 2.8399467E-02 energy calculations done at 11.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.57000 DelPhi exited at 16:00:24 11.571u 0.170s 0:12.02 97.6% 0+0k 0+0io 0pf+0w