Sat Oct 8 17:08:04 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 Sat Oct 8 2011 at 17:08:04 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3553 !!! WARNING: ASL 227 has a net charge of -0.1000 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: 0.5160243 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): -4.955000 64.03400 ymin,ymax (A): 13.95100 76.38300 zmin,zma (A): -13.03100 34.95700 x,y,z range (A): 68.98900 62.43200 47.98800 scale (grids/A): 0.5160243 object centre (A): 29.53950 45.16700 10.96300 number of atom coordinates read : 3553 total number of charged atoms : 3406 net assigned charge : -7.099985 assigned positive charge : 542.0941 centred at (gu) : 90.13297 87.74695 89.29391 assigned negative charge : -549.1959 centred at (gu) : 90.13902 87.80874 89.31879 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5903 nv = 96 ne = 84 npr = 72628 no. pairs analyzed = 72628 no. exposed pairs = 4372 no. arc points = 30556 no. surface atoms = 1469 nbur = 2084 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 = 1.652000 m= 216 mr = 3112 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3006 ## 477 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8015 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2832463E-11 -1.6162317E-10 midg,1,midg; midg,igrid,midg 4.5171530E-11 -1.6092302E-10 1,midg,midg; igrid,midg,midg -1.1257921E-10 -1.5163550E-10 gauss-seidel spectral radius is 0.9806980 estimated iterations to convergence 59 setup time was (sec) 0.6800000 now iterating at: 17:08:05 rms-change max change #iterations 6.1784431E-02 10.12126 at 10iterations 3.6062866E-03 0.5914288 at 20iterations 2.5808089E-04 4.6941757E-02 at 30iterations 4.3400789E-05 8.1739426E-03 at 40iterations 1.0683191E-05 2.0117760E-03 at 50iterations finished qdiffx linear iterations at : 17:08:09 total time elapsed so far: 4.440000 # loops : 50 mean,max change (kT/e) : 1.0683191E-05 2.0117760E-03 energy calculations done at 4.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 17:08:10 4.615u 0.389s 0:05.28 94.5% 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 Sat Oct 8 2011 at 17:08:10 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3553 !!! WARNING: ASL 227 has a net charge of -0.1000 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: 1.548073 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): -4.955000 64.03400 ymin,ymax (A): 13.95100 76.38300 zmin,zma (A): -13.03100 34.95700 x,y,z range (A): 68.98900 62.43200 47.98800 scale (grids/A): 1.548073 object centre (A): 29.53950 45.16700 10.96300 number of atom coordinates read : 3553 total number of charged atoms : 3406 net assigned charge : -7.099985 assigned positive charge : 542.0941 centred at (gu) : 90.39774 83.23990 87.88081 assigned negative charge : -549.1959 centred at (gu) : 90.41672 83.42603 87.95610 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30556 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19740 mr = 45798 m= 1811 mr = 13374 m= 35 mr = 843 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 133 time to turn everything in is 0.5500000 number of dielectric boundary points 28216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 458 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 25766 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) : 0.5160243 object centre at (A) : 29.53950 45.16700 10.96300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2759768E-04 -1.3942812E-03 midg,1,midg; midg,igrid,midg -1.4379305E-02 -1.4763611E-02 1,midg,midg; igrid,midg,midg 1.0282455E-02 -3.0957083E-03 gauss-seidel spectral radius is 0.9980161 estimated iterations to convergence 178 setup time was (sec) 0.9100000 now iterating at: 17:08:11 rms-change max change #iterations 3.295516 169.4324 at 10iterations 1.316622 56.11809 at 20iterations 0.5298392 19.39902 at 30iterations 0.2125669 8.013359 at 40iterations 8.5454933E-02 3.192001 at 50iterations 3.4201425E-02 1.225830 at 60iterations 1.3799654E-02 0.5858407 at 70iterations 5.5440264E-03 0.1902180 at 80iterations 2.2332522E-03 8.6942673E-02 at 90iterations 9.0380723E-04 3.1569004E-02 at 100iterations 3.7032363E-04 1.2092590E-02 at 110iterations 1.5478687E-04 5.5899620E-03 at 120iterations finished qdiffx linear iterations at : 17:08:21 total time elapsed so far: 11.19000 # loops : 120 mean,max change (kT/e) : 1.5478687E-04 5.5899620E-03 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 17:08:22 11.357u 0.450s 0:12.08 97.6% 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 Sat Oct 8 2011 at 17:08:22 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3553 !!! WARNING: ASL 227 has a net charge of -0.1000 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: 2.322109 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): -4.955000 64.03400 ymin,ymax (A): 13.95100 76.38300 zmin,zma (A): -13.03100 34.95700 x,y,z range (A): 68.98900 62.43200 47.98800 scale (grids/A): 2.322109 object centre (A): 29.53950 45.16700 10.96300 number of atom coordinates read : 3553 total number of charged atoms : 3406 net assigned charge : -7.099985 assigned positive charge : 542.0941 centred at (gu) : 90.59658 79.85950 86.82095 assigned negative charge : -549.1959 centred at (gu) : 90.62498 80.13898 86.93401 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 155502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30556 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70236 mr = 112606 m= 18133 mr = 55313 m= 2673 mr = 13226 m= 144 mr = 1692 m= 0 mr = 40 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 440 time to turn everything in is 1.370000 number of dielectric boundary points 63811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 27178 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) : 1.548073 object centre at (A) : 29.53950 45.16700 10.96300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3748212E-02 -1.4632848E-02 midg,1,midg; midg,igrid,midg -0.3031727 -0.2909828 1,midg,midg; igrid,midg,midg 0.4234092 -5.5074085E-02 gauss-seidel spectral radius is 0.9990893 estimated iterations to convergence 262 setup time was (sec) 1.710000 now iterating at: 17:08:24 rms-change max change #iterations 8.830590 290.2249 at 10iterations 4.900804 123.9623 at 20iterations 2.701282 68.82615 at 30iterations 1.480855 34.17004 at 40iterations 0.8103873 19.13893 at 50iterations 0.4400469 9.125916 at 60iterations 0.2391377 5.715065 at 70iterations 0.1301272 3.062888 at 80iterations 7.0606016E-02 1.470590 at 90iterations 3.8289063E-02 0.7758179 at 100iterations 2.0704823E-02 0.4556055 at 110iterations 1.1232423E-02 0.2499199 at 120iterations 6.0702167E-03 0.1266479 at 130iterations 3.2869459E-03 6.9250107E-02 at 140iterations 1.7792715E-03 3.6703110E-02 at 150iterations 9.6690940E-04 2.0431995E-02 at 160iterations 5.2462280E-04 1.0509014E-02 at 170iterations 2.8694098E-04 6.0324669E-03 at 180iterations finished qdiffx linear iterations at : 17:08:44 total time elapsed so far: 22.07000 # loops : 180 mean,max change (kT/e) : 2.8694098E-04 6.0324669E-03 energy calculations done at 22.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.24000 DelPhi exited at 17:08:45 22.242u 0.474s 0:22.99 98.7% 0+0k 0+0io 0pf+0w