Tue Nov 22 14:09:44 PST 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 Tue Nov 22 2011 at 14:09:49 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 = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5576004 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 0.5576004 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 285.3841 centred at (gu) : 89.72352 90.02395 89.15755 assigned negative charge : -280.3844 centred at (gu) : 89.63874 90.17416 89.12726 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4127 nv = 96 ne = 84 npr = 38388 no. pairs analyzed = 38388 no. exposed pairs = 2496 no. arc points = 17951 no. surface atoms = 852 nbur = 1096 mkacc time = 6.0000002E-02 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 = 1.540000 m= 178 mr = 2125 m= 0 mr = 7 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1872 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5202 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5875702E-10 5.6031985E-10 midg,1,midg; midg,igrid,midg 1.4281953E-09 -4.9356913E-10 1,midg,midg; igrid,midg,midg -6.4410574E-11 9.6257380E-10 gauss-seidel spectral radius is 0.9833332 estimated iterations to convergence 64 setup time was (sec) 0.3800000 now iterating at: 14:09:53 rms-change max change #iterations 6.3780583E-02 15.14012 at 10iterations 4.5004459E-03 0.8719082 at 20iterations 3.1432105E-04 6.2672615E-02 at 30iterations 2.1470389E-05 3.9567947E-03 at 40iterations 1.5161265E-06 2.6702881E-04 at 50iterations finished qdiffx linear iterations at : 14:10:02 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 1.5161265E-06 2.6702881E-04 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 14:10:04 3.747u 0.200s 0:16.67 23.6% 0+0k 0+0io 3pf+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 Tue Nov 22 2011 at 14:10:10 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 = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.672801 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 1.672801 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 285.3841 centred at (gu) : 89.17072 90.07183 87.47269 assigned negative charge : -280.3844 centred at (gu) : 88.91649 90.52290 87.38203 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 45048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15129 mr = 30058 m= 1874 mr = 10927 m= 62 mr = 1035 m= 0 mr = 4 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 222 time to turn everything in is 0.2500000 number of dielectric boundary points 20089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 14039 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) : 0.5576004 object centre at (A) : -11.41050 20.60050 29.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1940112E-02 2.0193782E-02 midg,1,midg; midg,igrid,midg 5.8931056E-03 -4.8221601E-03 1,midg,midg; igrid,midg,midg -9.2688133E-04 1.3588440E-03 gauss-seidel spectral radius is 0.9981585 estimated iterations to convergence 185 setup time was (sec) 0.4700000 now iterating at: 14:10:13 rms-change max change #iterations 2.714150 169.0049 at 10iterations 1.115722 52.50441 at 20iterations 0.4603349 21.05754 at 30iterations 0.1910132 7.887690 at 40iterations 7.8810923E-02 3.468404 at 50iterations 3.2821376E-02 1.414628 at 60iterations 1.3617405E-02 0.5935698 at 70iterations 5.6049968E-03 0.2508564 at 80iterations 2.3113175E-03 0.1107712 at 90iterations 9.6749712E-04 3.8301468E-02 at 100iterations 3.9876584E-04 1.8695831E-02 at 110iterations 1.6565120E-04 6.9293976E-03 at 120iterations finished qdiffx linear iterations at : 14:10:33 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 1.6565120E-04 6.9293976E-03 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 14:10:34 8.333u 0.269s 0:24.49 35.0% 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 Tue Nov 22 2011 at 14:10:36 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 = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.509202 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 2.509202 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 285.3841 centred at (gu) : 88.75614 90.10784 86.20897 assigned negative charge : -280.3844 centred at (gu) : 88.37467 90.78429 86.07297 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 104358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17951 grid for indexing accessible points = 1.400000 m= 50564 mr = 73254 m= 16365 mr = 40731 m= 3039 mr = 13028 m= 268 mr = 2109 m= 4 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 0.5800000 number of dielectric boundary points 45347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14534 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) : 1.672801 object centre at (A) : -11.41050 20.60050 29.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2850070 0.2106664 midg,1,midg; midg,igrid,midg 6.3938618E-02 -7.9742156E-02 1,midg,midg; igrid,midg,midg -2.9150745E-02 1.8078458E-02 gauss-seidel spectral radius is 0.9990982 estimated iterations to convergence 263 setup time was (sec) 0.8200000 now iterating at: 14:10:41 rms-change max change #iterations 6.770988 352.4458 at 10iterations 3.691997 99.17932 at 20iterations 2.001582 50.16912 at 30iterations 1.085396 25.76254 at 40iterations 0.5884937 14.92236 at 50iterations 0.3193681 8.161094 at 60iterations 0.1729519 4.079799 at 70iterations 9.3646303E-02 2.176010 at 80iterations 5.0529391E-02 1.162411 at 90iterations 2.7365608E-02 0.7404013 at 100iterations 1.4778604E-02 0.3519859 at 110iterations 8.0223288E-03 0.1897297 at 120iterations 4.3251091E-03 9.9735260E-02 at 130iterations 2.3444593E-03 5.8538675E-02 at 140iterations 1.2651889E-03 3.1669617E-02 at 150iterations 6.8349688E-04 1.5434265E-02 at 160iterations 3.6945846E-04 9.4408989E-03 at 170iterations 1.9977646E-04 4.6386719E-03 at 180iterations finished qdiffx linear iterations at : 14:11:16 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.9977646E-04 4.6386719E-03 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 14:11:18 12.886u 0.276s 0:41.95 31.3% 0+0k 0+0io 0pf+0w