Wed Dec 28 11:02:20 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+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 Wed Dec 28 2011 at 11:02:20 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! 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: 0.6240578 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): -35.26500 10.55700 ymin,ymax (A): 0.6140000 41.47000 zmin,zma (A): -0.3370000 56.70900 x,y,z range (A): 45.82200 40.85600 57.04600 scale (grids/A): 0.6240578 object centre (A): -12.35400 21.04200 28.18600 number of atom coordinates read : 1966 total number of charged atoms : 1766 net assigned charge : -19.95203 assigned positive charge : 267.1204 centred at (gu) : 90.28013 89.72083 89.83535 assigned negative charge : -287.0722 centred at (gu) : 90.21604 89.80901 89.85082 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5236 nv = 96 ne = 84 npr = 40237 no. pairs analyzed = 40237 no. exposed pairs = 2401 no. arc points = 16960 no. surface atoms = 813 nbur = 1153 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 2904 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1586 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7957758E-08 -1.8402774E-08 midg,1,midg; midg,igrid,midg -1.4166809E-08 -2.1784910E-08 1,midg,midg; igrid,midg,midg -2.0507288E-08 -1.5564451E-08 gauss-seidel spectral radius is 0.9866467 estimated iterations to convergence 71 setup time was (sec) 0.5300000 now iterating at: 11:02:21 rms-change max change #iterations 0.1177505 19.58046 at 10iterations 1.0843434E-02 1.787365 at 20iterations 1.0176364E-03 0.2034302 at 30iterations 9.4701842E-05 1.9201517E-02 at 40iterations 8.8025408E-06 1.3737679E-03 at 50iterations finished qdiffx linear iterations at : 11:02:25 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 8.8025408E-06 1.3737679E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 11:02:26 4.448u 0.402s 0:05.94 81.4% 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 28 2011 at 11:02:26 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.872173 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): -35.26500 10.55700 ymin,ymax (A): 0.6140000 41.47000 zmin,zma (A): -0.3370000 56.70900 x,y,z range (A): 45.82200 40.85600 57.04600 scale (grids/A): 1.872173 object centre (A): -12.35400 21.04200 28.18600 number of atom coordinates read : 1966 total number of charged atoms : 1766 net assigned charge : -19.95203 assigned positive charge : 267.1204 centred at (gu) : 90.84063 89.16264 89.50601 assigned negative charge : -287.0722 centred at (gu) : 90.64837 89.42717 89.55273 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 56656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 20986 mr = 39370 m= 3174 mr = 16025 m= 155 mr = 2011 m= 0 mr = 59 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 23506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 13918 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) : 0.6240578 object centre at (A) : -12.35400 21.04200 28.18600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6281874E-02 -5.4124713E-02 midg,1,midg; midg,igrid,midg -2.3781620E-02 -2.9684326E-02 1,midg,midg; igrid,midg,midg -2.4845039E-02 -3.4599163E-02 gauss-seidel spectral radius is 0.9985133 estimated iterations to convergence 206 setup time was (sec) 0.7900000 now iterating at: 11:02:27 rms-change max change #iterations 3.468369 144.6752 at 10iterations 1.580266 68.75857 at 20iterations 0.7117509 25.45215 at 30iterations 0.3238816 11.98916 at 40iterations 0.1465728 5.272079 at 50iterations 6.6151485E-02 2.641465 at 60iterations 3.0033320E-02 1.156308 at 70iterations 1.3583318E-02 0.4882933 at 80iterations 6.1642933E-03 0.2284131 at 90iterations 2.7927710E-03 9.9680901E-02 at 100iterations 1.2656046E-03 4.5785904E-02 at 110iterations 5.7317427E-04 2.2089005E-02 at 120iterations finished qdiffx linear iterations at : 11:02:36 total time elapsed so far: 9.950000 # loops : 120 mean,max change (kT/e) : 5.7317427E-04 2.2089005E-02 energy calculations done at 9.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.11000 DelPhi exited at 11:02:37 10.117u 0.430s 0:11.12 94.7% 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 28 2011 at 11:02:37 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.808260 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): -35.26500 10.55700 ymin,ymax (A): 0.6140000 41.47000 zmin,zma (A): -0.3370000 56.70900 x,y,z range (A): 45.82200 40.85600 57.04600 scale (grids/A): 2.808260 object centre (A): -12.35400 21.04200 28.18600 number of atom coordinates read : 1966 total number of charged atoms : 1766 net assigned charge : -19.95203 assigned positive charge : 267.1204 centred at (gu) : 91.26093 88.74393 89.25917 assigned negative charge : -287.0722 centred at (gu) : 90.97257 89.14072 89.32912 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 130703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 67575 mr = 95043 m= 25053 mr = 56243 m= 5636 mr = 20784 m= 670 mr = 4224 m= 41 mr = 466 m= 0 mr = 17 time to grow re-entrant surface = 0.7099999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 52901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 14126 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) : 1.872173 object centre at (A) : -12.35400 21.04200 28.18600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6697841 -0.7932871 midg,1,midg; midg,igrid,midg -0.2637380 -0.3200858 1,midg,midg; igrid,midg,midg -0.2712257 -0.3778789 gauss-seidel spectral radius is 0.9992077 estimated iterations to convergence 280 setup time was (sec) 1.530000 now iterating at: 11:02:39 rms-change max change #iterations 8.286547 344.9208 at 10iterations 4.762411 110.5603 at 20iterations 2.706034 67.95063 at 30iterations 1.535450 34.22453 at 40iterations 0.8666769 23.86666 at 50iterations 0.4881213 10.56433 at 60iterations 0.2755234 6.523519 at 70iterations 0.1560103 3.133453 at 80iterations 8.7477744E-02 1.649668 at 90iterations 4.9342252E-02 1.037308 at 100iterations 2.7783535E-02 0.5897048 at 110iterations 1.5630519E-02 0.3262978 at 120iterations 8.7984055E-03 0.1887932 at 130iterations 4.9565826E-03 9.6710205E-02 at 140iterations 2.7871116E-03 6.0722351E-02 at 150iterations 1.5672140E-03 3.2089710E-02 at 160iterations 8.8106189E-04 2.0843506E-02 at 170iterations 4.9621362E-04 9.5462799E-03 at 180iterations finished qdiffx linear iterations at : 11:02:56 total time elapsed so far: 18.27000 # loops : 180 mean,max change (kT/e) : 4.9621362E-04 9.5462799E-03 energy calculations done at 18.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.43000 DelPhi exited at 11:02:56 18.435u 0.458s 0:19.24 98.1% 0+0k 0+0io 0pf+0w