Mon Oct 10 19:37:48 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 Mon Oct 10 2011 at 19:37:48 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 = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6030627 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): 13.09200 72.12400 ymin,ymax (A): 3.935000 50.74000 zmin,zma (A): 5.778000 63.47900 x,y,z range (A): 59.03200 46.80500 57.70100 scale (grids/A): 0.6030627 object centre (A): 42.60800 27.33750 34.62850 number of atom coordinates read : 2896 total number of charged atoms : 2754 net assigned charge : -1.999968 assigned positive charge : 434.6770 centred at (gu) : 88.92969 90.04590 91.10965 assigned negative charge : -436.6782 centred at (gu) : 88.80616 90.16643 91.18456 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7045 nv = 96 ne = 84 npr = 57544 no. pairs analyzed = 57544 no. exposed pairs = 3891 no. arc points = 27724 no. surface atoms = 1302 nbur = 1594 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3592 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2793 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9440931E-09 -5.4472808E-09 midg,1,midg; midg,igrid,midg 4.4768509E-09 -6.3898802E-09 1,midg,midg; igrid,midg,midg -8.2673797E-09 3.6364696E-09 gauss-seidel spectral radius is 0.9858005 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 19:37:49 rms-change max change #iterations 0.1135765 16.75529 at 10iterations 9.8271053E-03 1.524350 at 20iterations 8.5562107E-04 0.1169395 at 30iterations 8.8176472E-05 1.4397979E-02 at 40iterations 1.5704589E-05 3.7035942E-03 at 50iterations finished qdiffx linear iterations at : 19:37:51 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.5704589E-05 3.7035942E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:37:52 3.385u 0.160s 0:04.06 87.1% 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 19:37:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 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: 1.809188 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): 13.09200 72.12400 ymin,ymax (A): 3.935000 50.74000 zmin,zma (A): 5.778000 63.47900 x,y,z range (A): 59.03200 46.80500 57.70100 scale (grids/A): 1.809188 object centre (A): 42.60800 27.33750 34.62850 number of atom coordinates read : 2896 total number of charged atoms : 2754 net assigned charge : -1.999968 assigned positive charge : 434.6770 centred at (gu) : 86.78812 90.13683 93.32803 assigned negative charge : -436.6782 centred at (gu) : 86.41813 90.49905 93.55336 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27724 grid for indexing accessible points = 1.400000 m= 24982 mr = 51113 m= 3232 mr = 17237 m= 147 mr = 1768 m= 0 mr = 41 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 492 time to turn everything in is 0.3600000 number of dielectric boundary points 34794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21577 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) : 0.6030627 object centre at (A) : 42.60800 27.33750 34.62850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7859448E-02 -1.5075408E-02 midg,1,midg; midg,igrid,midg 1.0018323E-02 -1.9845126E-02 1,midg,midg; igrid,midg,midg -4.6132788E-02 2.1072129E-02 gauss-seidel spectral radius is 0.9985318 estimated iterations to convergence 207 setup time was (sec) 0.5700000 now iterating at: 19:37:53 rms-change max change #iterations 4.063267 201.4523 at 10iterations 1.837623 60.60665 at 20iterations 0.8336123 27.08778 at 30iterations 0.3781711 13.50951 at 40iterations 0.1715111 5.519058 at 50iterations 7.8257196E-02 2.370036 at 60iterations 3.5488062E-02 1.183622 at 70iterations 1.6089557E-02 0.5023041 at 80iterations 7.3414268E-03 0.2373009 at 90iterations 3.3444124E-03 0.1071720 at 100iterations 1.5199259E-03 4.8526764E-02 at 110iterations 6.9576374E-04 2.4030685E-02 at 120iterations finished qdiffx linear iterations at : 19:38:00 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 6.9576374E-04 2.4030685E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 19:38:00 7.771u 0.207s 0:08.26 96.4% 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 19:38:00 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 = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.713782 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): 13.09200 72.12400 ymin,ymax (A): 3.935000 50.74000 zmin,zma (A): 5.778000 63.47900 x,y,z range (A): 59.03200 46.80500 57.70100 scale (grids/A): 2.713782 object centre (A): 42.60800 27.33750 34.62850 number of atom coordinates read : 2896 total number of charged atoms : 2754 net assigned charge : -1.999968 assigned positive charge : 434.6770 centred at (gu) : 85.18204 90.20489 94.99183 assigned negative charge : -436.6782 centred at (gu) : 84.62698 90.74850 95.33001 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 177548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27724 grid for indexing accessible points = 1.400000 m= 82836 mr = 124588 m= 26711 mr = 65610 m= 5299 mr = 20236 m= 601 mr = 3662 m= 32 mr = 368 m= 0 mr = 5 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 1673 time to turn everything in is 0.9300000 number of dielectric boundary points 78558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 22031 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) : 1.809188 object centre at (A) : 42.60800 27.33750 34.62850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1848794 1.2917537E-02 midg,1,midg; midg,igrid,midg 0.1012750 -0.1958641 1,midg,midg; igrid,midg,midg -0.6001379 0.2608146 gauss-seidel spectral radius is 0.9992528 estimated iterations to convergence 289 setup time was (sec) 1.160000 now iterating at: 19:38:02 rms-change max change #iterations 10.12331 285.8247 at 10iterations 6.018621 168.1707 at 20iterations 3.542091 85.60039 at 30iterations 2.062428 48.06150 at 40iterations 1.201248 27.53406 at 50iterations 0.6940553 14.89305 at 60iterations 0.4017712 8.984857 at 70iterations 0.2315910 4.557350 at 80iterations 0.1334130 3.116756 at 90iterations 7.6689094E-02 1.556011 at 100iterations 4.4093531E-02 0.8161893 at 110iterations 2.5357520E-02 0.4897280 at 120iterations 1.4546860E-02 0.2686663 at 130iterations 8.3424132E-03 0.1666794 at 140iterations 4.7891028E-03 9.0253115E-02 at 150iterations 2.7538151E-03 4.9476624E-02 at 160iterations 1.5804117E-03 3.2911301E-02 at 170iterations 9.0914790E-04 1.9338608E-02 at 180iterations finished qdiffx linear iterations at : 19:38:13 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 9.0914790E-04 1.9338608E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 19:38:13 12.620u 0.209s 0:13.10 97.8% 0+0k 0+0io 0pf+0w