Sun Oct 9 17:12:42 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 17:12:42 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3258 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5718876 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): -11.12100 51.12900 ymin,ymax (A): -12.43600 40.32700 zmin,zma (A): 20.22800 76.06800 x,y,z range (A): 62.25000 52.76300 55.84000 scale (grids/A): 0.5718876 object centre (A): 20.00400 13.94550 48.14800 number of atom coordinates read : 3258 total number of charged atoms : 3129 net assigned charge : 4.621026 assigned positive charge : 506.1989 centred at (gu) : 91.07010 89.85901 88.02814 assigned negative charge : -501.5791 centred at (gu) : 90.91883 89.96558 87.96069 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7130 nv = 96 ne = 84 npr = 62735 no. pairs analyzed = 62735 no. exposed pairs = 4429 no. arc points = 31361 no. surface atoms = 1483 nbur = 1775 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 336 mr = 3520 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3033 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8923 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8718077E-10 1.2645486E-09 midg,1,midg; midg,igrid,midg 2.8202418E-09 -1.2369883E-09 1,midg,midg; igrid,midg,midg -1.6538733E-09 4.5805288E-09 gauss-seidel spectral radius is 0.9842501 estimated iterations to convergence 65 setup time was (sec) 0.6800000 now iterating at: 17:12:43 rms-change max change #iterations 9.6027978E-02 15.17603 at 10iterations 7.2564282E-03 1.236145 at 20iterations 6.6392397E-04 0.1114235 at 30iterations 1.8972156E-04 2.6909828E-02 at 40iterations 9.6338073E-05 1.4113426E-02 at 50iterations finished qdiffx linear iterations at : 17:12:46 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 9.6338073E-05 1.4113426E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 17:12:47 4.124u 0.258s 0:04.76 91.8% 0+0k 0+0io 6pf+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 17:12:47 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3258 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.715663 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): -11.12100 51.12900 ymin,ymax (A): -12.43600 40.32700 zmin,zma (A): 20.22800 76.06800 x,y,z range (A): 62.25000 52.76300 55.84000 scale (grids/A): 1.715663 object centre (A): 20.00400 13.94550 48.14800 number of atom coordinates read : 3258 total number of charged atoms : 3129 net assigned charge : 4.621026 assigned positive charge : 506.1989 centred at (gu) : 93.20908 89.57606 84.08350 assigned negative charge : -501.5791 centred at (gu) : 92.75607 89.89630 83.88172 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77618 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31361 grid for indexing accessible points = 1.400000 m= 26137 mr = 51356 m= 3281 mr = 17662 m= 110 mr = 1562 m= 0 mr = 6 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 36560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 24226 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) : 0.5718876 object centre at (A) : 20.00400 13.94550 48.14800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7550596E-03 7.8689391E-03 midg,1,midg; midg,igrid,midg 1.8093642E-02 -9.2930654E-03 1,midg,midg; igrid,midg,midg -5.7742861E-03 2.4304871E-02 gauss-seidel spectral radius is 0.9983962 estimated iterations to convergence 198 setup time was (sec) 1.020000 now iterating at: 17:12:48 rms-change max change #iterations 3.990744 164.8548 at 10iterations 1.752488 63.83329 at 20iterations 0.7719662 24.78955 at 30iterations 0.3398244 11.23434 at 40iterations 0.1503128 5.324539 at 50iterations 6.6146009E-02 2.144864 at 60iterations 2.9226886E-02 0.9700661 at 70iterations 1.2847938E-02 0.4184608 at 80iterations 5.6753033E-03 0.1883926 at 90iterations 2.4959475E-03 7.7743530E-02 at 100iterations 1.1049868E-03 4.0783592E-02 at 110iterations 4.8830506E-04 1.8060522E-02 at 120iterations finished qdiffx linear iterations at : 17:12:56 total time elapsed so far: 9.330000 # loops : 120 mean,max change (kT/e) : 4.8830506E-04 1.8060522E-02 energy calculations done at 9.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 17:12:57 9.512u 0.275s 0:10.06 97.2% 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 17:12:57 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3258 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.573494 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): -11.12100 51.12900 ymin,ymax (A): -12.43600 40.32700 zmin,zma (A): 20.22800 76.06800 x,y,z range (A): 62.25000 52.76300 55.84000 scale (grids/A): 2.573494 object centre (A): 20.00400 13.94550 48.14800 number of atom coordinates read : 3258 total number of charged atoms : 3129 net assigned charge : 4.621026 assigned positive charge : 506.1989 centred at (gu) : 94.81350 89.36367 81.12516 assigned negative charge : -501.5791 centred at (gu) : 94.13395 89.84435 80.82266 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 179747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31361 grid for indexing accessible points = 1.400000 m= 86506 mr = 126254 m= 28284 mr = 67321 m= 5275 mr = 20903 m= 485 mr = 3283 m= 13 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 82327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 25021 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) : 1.715663 object centre at (A) : 20.00400 13.94550 48.14800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1381589 8.2064554E-02 midg,1,midg; midg,igrid,midg 0.2702886 -0.1967196 1,midg,midg; igrid,midg,midg 0.1293807 0.2723949 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 2.070000 now iterating at: 17:12:59 rms-change max change #iterations 10.28871 296.9452 at 10iterations 6.073561 185.7216 at 20iterations 3.538920 82.54202 at 30iterations 2.046718 46.09904 at 40iterations 1.182324 25.35575 at 50iterations 0.6773368 13.78405 at 60iterations 0.3873858 8.646336 at 70iterations 0.2218014 4.907063 at 80iterations 0.1263357 2.592406 at 90iterations 7.2029807E-02 1.452700 at 100iterations 4.0942647E-02 0.8583870 at 110iterations 2.3343725E-02 0.4618673 at 120iterations 1.3269418E-02 0.2772269 at 130iterations 7.5675002E-03 0.1589203 at 140iterations 4.3295496E-03 8.2221031E-02 at 150iterations 2.5012249E-03 4.5882225E-02 at 160iterations 1.4756529E-03 3.1282425E-02 at 170iterations 9.1083418E-04 1.8789768E-02 at 180iterations finished qdiffx linear iterations at : 17:13:13 total time elapsed so far: 15.84000 # loops : 180 mean,max change (kT/e) : 9.1083418E-04 1.8789768E-02 energy calculations done at 15.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.02000 DelPhi exited at 17:13:14 16.024u 0.315s 0:16.62 98.2% 0+0k 0+0io 0pf+0w