Sat Oct 8 23:56:05 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 Sat Oct 8 2011 at 23:56:05 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 = 2428 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: 0.6461566 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): -13.99900 41.09600 ymin,ymax (A): -30.79700 23.63200 zmin,zma (A): -9.573000 32.62100 x,y,z range (A): 55.09500 54.42900 42.19400 scale (grids/A): 0.6461566 object centre (A): 13.54850 -3.582500 11.52400 number of atom coordinates read : 2428 total number of charged atoms : 2293 net assigned charge : 12.00002 assigned positive charge : 352.8462 centred at (gu) : 89.84597 91.31802 90.82150 assigned negative charge : -340.8470 centred at (gu) : 89.80412 91.29543 90.75941 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6969 nv = 96 ne = 84 npr = 48374 no. pairs analyzed = 48374 no. exposed pairs = 3200 no. arc points = 23070 no. surface atoms = 1068 nbur = 1360 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 3689 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1165350E-08 3.3371226E-08 midg,1,midg; midg,igrid,midg 1.3757447E-08 3.0750122E-08 1,midg,midg; igrid,midg,midg 1.6084529E-08 2.4892435E-08 gauss-seidel spectral radius is 0.9875827 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 23:56:06 rms-change max change #iterations 0.1372471 22.92279 at 10iterations 1.3987738E-02 2.012640 at 20iterations 1.6422896E-03 0.2258453 at 30iterations 3.2969707E-04 6.0018539E-02 at 40iterations 1.0699302E-04 2.1640778E-02 at 50iterations finished qdiffx linear iterations at : 23:56:09 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.0699302E-04 2.1640778E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 23:56:09 3.337u 0.170s 0:03.79 92.3% 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 8 2011 at 23:56:09 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 = 2428 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: 1.938470 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): -13.99900 41.09600 ymin,ymax (A): -30.79700 23.63200 zmin,zma (A): -9.573000 32.62100 x,y,z range (A): 55.09500 54.42900 42.19400 scale (grids/A): 1.938470 object centre (A): 13.54850 -3.582500 11.52400 number of atom coordinates read : 2428 total number of charged atoms : 2293 net assigned charge : 12.00002 assigned positive charge : 352.8462 centred at (gu) : 89.53760 93.95345 92.46407 assigned negative charge : -340.8470 centred at (gu) : 89.41226 93.88610 92.27823 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74692 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23070 grid for indexing accessible points = 1.400000 m= 26736 mr = 50388 m= 4636 mr = 19319 m= 337 mr = 2867 m= 8 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 979 time to turn everything in is 0.3600000 number of dielectric boundary points 33698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18089 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) : 0.6461566 object centre at (A) : 13.54850 -3.582500 11.52400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4781230E-03 3.2276496E-02 midg,1,midg; midg,igrid,midg 3.9055504E-02 2.5855940E-02 1,midg,midg; igrid,midg,midg 5.6642532E-02 5.4791834E-02 gauss-seidel spectral radius is 0.9986722 estimated iterations to convergence 217 setup time was (sec) 0.5800000 now iterating at: 23:56:10 rms-change max change #iterations 4.044216 189.0089 at 10iterations 1.905546 70.58925 at 20iterations 0.9033043 27.77129 at 30iterations 0.4253171 16.24263 at 40iterations 0.2003902 6.491291 at 50iterations 9.5361747E-02 3.112022 at 60iterations 4.5082863E-02 1.397648 at 70iterations 2.1391880E-02 0.6483612 at 80iterations 1.0131162E-02 0.3139353 at 90iterations 4.8686066E-03 0.1580558 at 100iterations 2.3575057E-03 7.6255798E-02 at 110iterations 1.1815615E-03 4.1503906E-02 at 120iterations finished qdiffx linear iterations at : 23:56:17 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.1815615E-03 4.1503906E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 23:56:17 7.698u 0.198s 0:08.26 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 8 2011 at 23:56:17 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 = 2428 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: 2.907705 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): -13.99900 41.09600 ymin,ymax (A): -30.79700 23.63200 zmin,zma (A): -9.573000 32.62100 x,y,z range (A): 55.09500 54.42900 42.19400 scale (grids/A): 2.907705 object centre (A): 13.54850 -3.582500 11.52400 number of atom coordinates read : 2428 total number of charged atoms : 2293 net assigned charge : 12.00002 assigned positive charge : 352.8462 centred at (gu) : 89.30630 95.93006 93.69595 assigned negative charge : -340.8470 centred at (gu) : 89.11835 95.82908 93.41732 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 172476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23070 grid for indexing accessible points = 1.400000 m= 85779 mr = 122515 m= 31968 mr = 69014 m= 8349 mr = 25380 m= 1379 mr = 6249 m= 117 mr = 940 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 3212 time to turn everything in is 0.9400000 number of dielectric boundary points 75920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 18344 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) : 1.938470 object centre at (A) : 13.54850 -3.582500 11.52400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9326689E-02 0.3148097 midg,1,midg; midg,igrid,midg 0.5546752 0.2909351 1,midg,midg; igrid,midg,midg 0.5623099 0.5032050 gauss-seidel spectral radius is 0.9992739 estimated iterations to convergence 293 setup time was (sec) 1.170000 now iterating at: 23:56:19 rms-change max change #iterations 9.658418 659.6387 at 10iterations 5.717905 155.2601 at 20iterations 3.345930 82.06081 at 30iterations 1.958726 41.63205 at 40iterations 1.142599 24.08557 at 50iterations 0.6656017 13.16503 at 60iterations 0.3885460 7.571365 at 70iterations 0.2254819 4.724852 at 80iterations 0.1306904 2.512831 at 90iterations 7.5966813E-02 1.465741 at 100iterations 4.4034529E-02 0.7840233 at 110iterations 2.5566751E-02 0.5543466 at 120iterations 1.4823781E-02 0.2727470 at 130iterations 8.6102448E-03 0.1566467 at 140iterations 5.0238101E-03 9.4938278E-02 at 150iterations 2.9620673E-03 6.0049057E-02 at 160iterations 1.7767238E-03 3.6247253E-02 at 170iterations 1.0993680E-03 2.4398804E-02 at 180iterations finished qdiffx linear iterations at : 23:56:30 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 1.0993680E-03 2.4398804E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 23:56:30 12.467u 0.203s 0:12.96 97.6% 0+0k 0+0io 0pf+0w