Tue Oct 11 08:25:12 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 Tue Oct 11 2011 at 08:25:12 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6419504 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): -12.14900 37.01700 ymin,ymax (A): -27.33100 21.00000 zmin,zma (A): -9.732000 45.72400 x,y,z range (A): 49.16600 48.33100 55.45600 scale (grids/A): 0.6419504 object centre (A): 12.43400 -3.165500 17.99600 number of atom coordinates read : 2826 total number of charged atoms : 2663 net assigned charge : 1.701017 assigned positive charge : 427.0639 centred at (gu) : 90.08782 90.75661 91.58038 assigned negative charge : -425.3632 centred at (gu) : 89.85312 90.62030 91.52986 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7799 nv = 96 ne = 84 npr = 57123 no. pairs analyzed = 57123 no. exposed pairs = 3358 no. arc points = 23377 no. surface atoms = 1132 nbur = 1694 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4503 m= 3 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3300000 number of dielectric boundary points 3658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2263 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1439826E-09 1.2832698E-08 midg,1,midg; midg,igrid,midg -1.3763275E-08 2.4061945E-08 1,midg,midg; igrid,midg,midg -2.9445296E-08 3.3760696E-08 gauss-seidel spectral radius is 0.9874442 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 08:25:13 rms-change max change #iterations 0.1584704 23.52234 at 10iterations 1.6620653E-02 2.189286 at 20iterations 2.0497355E-03 0.2639360 at 30iterations 4.2451255E-04 5.3638458E-02 at 40iterations 1.3602016E-04 1.7501831E-02 at 50iterations finished qdiffx linear iterations at : 08:25:16 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.3602016E-04 1.7501831E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:25:16 3.373u 0.158s 0:03.96 88.8% 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 Oct 11 2011 at 08:25:16 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.925851 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): -12.14900 37.01700 ymin,ymax (A): -27.33100 21.00000 zmin,zma (A): -9.732000 45.72400 x,y,z range (A): 49.16600 48.33100 55.45600 scale (grids/A): 1.925851 object centre (A): 12.43400 -3.165500 17.99600 number of atom coordinates read : 2826 total number of charged atoms : 2663 net assigned charge : 1.701017 assigned positive charge : 427.0639 centred at (gu) : 90.26281 92.26937 94.74037 assigned negative charge : -425.3632 centred at (gu) : 89.55914 91.86069 94.58932 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 83882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23377 grid for indexing accessible points = 1.400000 m= 31910 mr = 59749 m= 5358 mr = 24267 m= 385 mr = 3536 m= 9 mr = 182 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 607 time to turn everything in is 0.6500000 number of dielectric boundary points 33808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20995 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) : 0.6419504 object centre at (A) : 12.43400 -3.165500 17.99600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2486230E-02 8.6837737E-03 midg,1,midg; midg,igrid,midg -8.5660433E-03 1.4028491E-02 1,midg,midg; igrid,midg,midg -1.5571212E-02 5.3670384E-02 gauss-seidel spectral radius is 0.9986855 estimated iterations to convergence 219 setup time was (sec) 0.9200000 now iterating at: 08:25:17 rms-change max change #iterations 4.577219 166.2004 at 10iterations 2.185030 66.79845 at 20iterations 1.043042 35.64288 at 30iterations 0.4964567 14.37448 at 40iterations 0.2370957 7.461234 at 50iterations 0.1127689 3.622312 at 60iterations 5.3825382E-02 1.595055 at 70iterations 2.5690239E-02 0.7804699 at 80iterations 1.2343508E-02 0.3735657 at 90iterations 5.9731351E-03 0.1709824 at 100iterations 2.9234269E-03 8.3244324E-02 at 110iterations 1.4764549E-03 4.3510437E-02 at 120iterations finished qdiffx linear iterations at : 08:25:24 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.4764549E-03 4.3510437E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 08:25:25 7.699u 0.177s 0:08.45 93.0% 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 Oct 11 2011 at 08:25:25 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.888777 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): -12.14900 37.01700 ymin,ymax (A): -27.33100 21.00000 zmin,zma (A): -9.732000 45.72400 x,y,z range (A): 49.16600 48.33100 55.45600 scale (grids/A): 2.888777 object centre (A): 12.43400 -3.165500 17.99600 number of atom coordinates read : 2826 total number of charged atoms : 2663 net assigned charge : 1.701017 assigned positive charge : 427.0639 centred at (gu) : 90.39416 93.40370 97.11037 assigned negative charge : -425.3632 centred at (gu) : 89.33858 92.79097 96.88380 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 193678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23377 grid for indexing accessible points = 1.400000 m= 102385 mr = 143842 m= 38449 mr = 85426 m= 9860 mr = 31818 m= 1716 mr = 7713 m= 163 mr = 1256 m= 6 mr = 101 m= 0 mr = 3 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 2097 time to turn everything in is 1.570000 number of dielectric boundary points 76098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 21302 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) : 1.925851 object centre at (A) : 12.43400 -3.165500 17.99600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5984381 0.2892689 midg,1,midg; midg,igrid,midg -0.1058517 0.1794681 1,midg,midg; igrid,midg,midg -0.1558326 0.4728923 gauss-seidel spectral radius is 0.9992705 estimated iterations to convergence 292 setup time was (sec) 1.870000 now iterating at: 08:25:27 rms-change max change #iterations 10.60595 344.4382 at 10iterations 6.209453 133.8128 at 20iterations 3.613523 83.95023 at 30iterations 2.102074 39.49883 at 40iterations 1.222118 20.78048 at 50iterations 0.7092856 12.65886 at 60iterations 0.4111494 6.842964 at 70iterations 0.2380984 4.605490 at 80iterations 0.1379047 2.464845 at 90iterations 7.9809599E-02 1.398531 at 100iterations 4.6244968E-02 0.8157139 at 110iterations 2.6859136E-02 0.4480743 at 120iterations 1.5576658E-02 0.2718506 at 130iterations 9.0681408E-03 0.1550975 at 140iterations 5.3150021E-03 9.5653534E-02 at 150iterations 3.1594397E-03 5.7509899E-02 at 160iterations 1.9080720E-03 3.5301208E-02 at 170iterations 1.1854651E-03 1.9996643E-02 at 180iterations finished qdiffx linear iterations at : 08:25:37 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 1.1854651E-03 1.9996643E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 08:25:38 12.519u 0.186s 0:13.13 96.6% 0+0k 0+0io 0pf+0w