Mon Oct 10 16:20:28 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 16:20:28 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3112 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: 0.5679371 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): -4.523000 55.17600 ymin,ymax (A): 35.67000 98.35300 zmin,zma (A): 155.9210 215.0610 x,y,z range (A): 59.69900 62.68299 59.14000 scale (grids/A): 0.5679371 object centre (A): 25.32650 67.01150 185.4910 number of atom coordinates read : 3112 total number of charged atoms : 2964 net assigned charge : 14.50003 assigned positive charge : 477.2158 centred at (gu) : 90.77534 91.31316 90.80136 assigned negative charge : -462.7172 centred at (gu) : 90.72646 91.30402 90.88857 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6798 nv = 96 ne = 84 npr = 57430 no. pairs analyzed = 57430 no. exposed pairs = 4448 no. arc points = 33798 no. surface atoms = 1481 nbur = 1631 mkacc time = 0.1600000 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 = 1.512000 m= 296 mr = 3001 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3517 ## 473 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7945646E-09 8.5618568E-10 midg,1,midg; midg,igrid,midg 1.4243907E-09 2.9919032E-09 1,midg,midg; igrid,midg,midg 1.1060707E-09 3.3609340E-09 gauss-seidel spectral radius is 0.9840401 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 16:20:29 rms-change max change #iterations 8.9368843E-02 17.87838 at 10iterations 6.5732645E-03 1.100304 at 20iterations 4.8300563E-04 8.8836670E-02 at 30iterations 3.8397564E-05 5.6982040E-03 at 40iterations 3.7214193E-06 5.5503845E-04 at 50iterations finished qdiffx linear iterations at : 16:20:32 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 3.7214193E-06 5.5503845E-04 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 16:20:33 4.124u 0.250s 0:04.65 93.9% 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 16:20:33 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3112 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: 1.703811 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): -4.523000 55.17600 ymin,ymax (A): 35.67000 98.35300 zmin,zma (A): 155.9210 215.0610 x,y,z range (A): 59.69900 62.68299 59.14000 scale (grids/A): 1.703811 object centre (A): 25.32650 67.01150 185.4910 number of atom coordinates read : 3112 total number of charged atoms : 2964 net assigned charge : 14.50003 assigned positive charge : 477.2158 centred at (gu) : 92.32515 93.93855 92.40352 assigned negative charge : -462.7172 centred at (gu) : 92.17909 93.91167 92.66538 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33798 grid for indexing accessible points = 1.400000 m= 23014 mr = 44540 m= 2857 mr = 15399 m= 107 mr = 1332 m= 0 mr = 15 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1205 time to turn everything in is 0.6600000 number of dielectric boundary points 37917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 387 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 22925 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) : 0.5679371 object centre at (A) : 25.32650 67.01150 185.4910 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1970624E-02 2.6014935E-02 midg,1,midg; midg,igrid,midg -3.3689395E-03 2.4846576E-02 1,midg,midg; igrid,midg,midg 2.0448152E-02 1.2425612E-02 gauss-seidel spectral radius is 0.9983835 estimated iterations to convergence 197 setup time was (sec) 0.9500000 now iterating at: 16:20:34 rms-change max change #iterations 3.763176 172.7835 at 10iterations 1.613547 60.78764 at 20iterations 0.7048002 27.16108 at 30iterations 0.3047425 10.53062 at 40iterations 0.1324214 4.431757 at 50iterations 5.8006160E-02 2.141832 at 60iterations 2.5235588E-02 0.9128933 at 70iterations 1.1024584E-02 0.3728690 at 80iterations 4.8114583E-03 0.1582017 at 90iterations 2.1108615E-03 7.6066971E-02 at 100iterations 9.1986713E-04 3.1208038E-02 at 110iterations 4.0278118E-04 1.4279366E-02 at 120iterations finished qdiffx linear iterations at : 16:20:42 total time elapsed so far: 9.290000 # loops : 120 mean,max change (kT/e) : 4.0278118E-04 1.4279366E-02 energy calculations done at 9.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 16:20:43 9.474u 0.298s 0:10.13 96.3% 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 Mon Oct 10 2011 at 16:20:43 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3112 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: 2.555717 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): -4.523000 55.17600 ymin,ymax (A): 35.67000 98.35300 zmin,zma (A): 155.9210 215.0610 x,y,z range (A): 59.69900 62.68299 59.14000 scale (grids/A): 2.555717 object centre (A): 25.32650 67.01150 185.4910 number of atom coordinates read : 3112 total number of charged atoms : 2964 net assigned charge : 14.50003 assigned positive charge : 477.2158 centred at (gu) : 93.48732 95.90761 93.60488 assigned negative charge : -462.7172 centred at (gu) : 93.26853 95.86731 93.99809 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 169290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33798 grid for indexing accessible points = 1.400000 m= 75894 mr = 109710 m= 24305 mr = 58209 m= 4408 mr = 17881 m= 367 mr = 2693 m= 5 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 4379 time to turn everything in is 1.620000 number of dielectric boundary points 85622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 23692 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) : 1.703811 object centre at (A) : 25.32650 67.01150 185.4910 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1308280 0.3099406 midg,1,midg; midg,igrid,midg -0.5759926 0.3362649 1,midg,midg; igrid,midg,midg 0.1790518 -0.1343330 gauss-seidel spectral radius is 0.9992146 estimated iterations to convergence 282 setup time was (sec) 1.950000 now iterating at: 16:20:45 rms-change max change #iterations 9.585539 368.8436 at 10iterations 5.575019 145.2575 at 20iterations 3.211879 77.60665 at 30iterations 1.842064 42.50387 at 40iterations 1.053212 23.59909 at 50iterations 0.6002830 12.32473 at 60iterations 0.3407102 6.596619 at 70iterations 0.1935564 4.004478 at 80iterations 0.1097084 2.400757 at 90iterations 6.2108409E-02 1.158001 at 100iterations 3.5126213E-02 0.8046570 at 110iterations 1.9874059E-02 0.3987255 at 120iterations 1.1224718E-02 0.2134218 at 130iterations 6.3513066E-03 0.1364040 at 140iterations 3.5738831E-03 6.8786621E-02 at 150iterations 2.0205232E-03 3.8578033E-02 at 160iterations 1.1421021E-03 2.2440910E-02 at 170iterations 6.4480706E-04 1.2886047E-02 at 180iterations finished qdiffx linear iterations at : 16:20:59 total time elapsed so far: 15.82000 # loops : 180 mean,max change (kT/e) : 6.4480706E-04 1.2886047E-02 energy calculations done at 15.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.99000 DelPhi exited at 16:20:59 15.993u 0.306s 0:16.58 98.2% 0+0k 0+0io 0pf+0w