Wed Dec 21 14:21:09 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 Wed Dec 21 2011 at 14:21:09 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 0.6188614 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): -35.19000 10.02100 ymin,ymax (A): 1.031000 41.24700 zmin,zma (A): -2.201000 55.32400 x,y,z range (A): 45.21100 40.21600 57.52500 scale (grids/A): 0.6188614 object centre (A): -12.58450 21.13900 26.56150 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 263.8705 centred at (gu) : 90.38005 89.68649 90.81963 assigned negative charge : -285.8223 centred at (gu) : 90.29846 89.84511 90.83591 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5165 nv = 96 ne = 84 npr = 40054 no. pairs analyzed = 40054 no. exposed pairs = 2411 no. arc points = 16798 no. surface atoms = 822 nbur = 1138 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 2867 m= 0 mr = 52 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1629 ## 115 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3718410E-08 -2.1294429E-08 midg,1,midg; midg,igrid,midg -1.0350960E-08 -2.3109143E-08 1,midg,midg; igrid,midg,midg -1.9338955E-08 -1.4360575E-08 gauss-seidel spectral radius is 0.9864237 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 14:21:10 rms-change max change #iterations 0.1121398 19.04612 at 10iterations 1.0165903E-02 1.874695 at 20iterations 9.3693723E-04 0.1670790 at 30iterations 8.4573905E-05 1.4032364E-02 at 40iterations 7.6621809E-06 1.2092590E-03 at 50iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 7.020000 # loops : 50 mean,max change (kT/e) : 7.6621809E-06 1.2092590E-03 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 14:21:19 7.230u 0.482s 0:11.24 68.5% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:21 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 1.856584 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): -35.19000 10.02100 ymin,ymax (A): 1.031000 41.24700 zmin,zma (A): -2.201000 55.32400 x,y,z range (A): 45.21100 40.21600 57.52500 scale (grids/A): 1.856584 object centre (A): -12.58450 21.13900 26.56150 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 263.8705 centred at (gu) : 91.14058 89.06013 92.45931 assigned negative charge : -285.8223 centred at (gu) : 90.89557 89.53545 92.50768 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 55436 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16798 grid for indexing accessible points = 1.400000 m= 20621 mr = 38512 m= 3259 mr = 15691 m= 209 mr = 2175 m= 1 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.4700000 number of dielectric boundary points 23063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 13825 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) : 0.6188614 object centre at (A) : -12.58450 21.13900 26.56150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7040919E-02 -6.5281540E-02 midg,1,midg; midg,igrid,midg -2.2496106E-02 -3.8471054E-02 1,midg,midg; igrid,midg,midg -2.3604803E-02 -3.1106630E-02 gauss-seidel spectral radius is 0.9984886 estimated iterations to convergence 204 setup time was (sec) 0.8400000 now iterating at: 14:21:23 rms-change max change #iterations 3.402888 168.7648 at 10iterations 1.529774 60.84246 at 20iterations 0.6855878 24.40418 at 30iterations 0.3116922 11.08625 at 40iterations 0.1391684 4.854675 at 50iterations 6.2821619E-02 2.234921 at 60iterations 2.8147489E-02 1.006754 at 70iterations 1.2718447E-02 0.4703274 at 80iterations 5.7054041E-03 0.2139058 at 90iterations 2.5741309E-03 8.8625908E-02 at 100iterations 1.1607741E-03 4.2802811E-02 at 110iterations 5.2255392E-04 2.0051956E-02 at 120iterations finished qdiffx linear iterations at : 14:21:40 total time elapsed so far: 18.30000 # loops : 120 mean,max change (kT/e) : 5.2255392E-04 2.0051956E-02 energy calculations done at 18.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.47000 DelPhi exited at 14:21:44 18.475u 0.629s 0:23.09 82.6% 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 Wed Dec 21 2011 at 14:21:45 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 2.784876 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): -35.19000 10.02100 ymin,ymax (A): 1.031000 41.24700 zmin,zma (A): -2.201000 55.32400 x,y,z range (A): 45.21100 40.21600 57.52500 scale (grids/A): 2.784876 object centre (A): -12.58450 21.13900 26.56150 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 263.8705 centred at (gu) : 91.71081 88.59051 93.68902 assigned negative charge : -285.8223 centred at (gu) : 91.34335 89.30320 93.76157 start vw surface at 0.1000000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 127706 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16798 grid for indexing accessible points = 1.400000 m= 66399 mr = 92772 m= 24650 mr = 55132 m= 5899 mr = 20378 m= 844 mr = 4659 m= 54 mr = 611 m= 0 mr = 25 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 861 time to turn everything in is 1.250000 number of dielectric boundary points 51975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 14076 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) : 1.856584 object centre at (A) : -12.58450 21.13900 26.56150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5245309 -0.8896886 midg,1,midg; midg,igrid,midg -0.2633919 -0.4172198 1,midg,midg; igrid,midg,midg -0.2510003 -0.3367634 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 1.630000 now iterating at: 14:21:47 rms-change max change #iterations 7.979049 385.8884 at 10iterations 4.530321 136.0527 at 20iterations 2.561275 68.30368 at 30iterations 1.443152 30.80004 at 40iterations 0.8099874 16.94934 at 50iterations 0.4566619 10.73262 at 60iterations 0.2566437 5.282763 at 70iterations 0.1438408 3.119057 at 80iterations 8.0526933E-02 1.644699 at 90iterations 4.5197081E-02 1.041870 at 100iterations 2.5375854E-02 0.4912529 at 110iterations 1.4235111E-02 0.3136377 at 120iterations 8.0006178E-03 0.1790152 at 130iterations 4.4834549E-03 9.0120316E-02 at 140iterations 2.5116664E-03 4.7292709E-02 at 150iterations 1.4100238E-03 3.3607483E-02 at 160iterations 7.9195015E-04 1.5773773E-02 at 170iterations 4.4315588E-04 1.0391235E-02 at 180iterations finished qdiffx linear iterations at : 14:22:18 total time elapsed so far: 32.21000 # loops : 180 mean,max change (kT/e) : 4.4315588E-04 1.0391235E-02 energy calculations done at 32.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 32.38000 DelPhi exited at 14:22:25 32.381u 0.574s 0:40.86 80.6% 0+0k 0+0io 0pf+0w