Wed Dec 21 14:21:11 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 14:21:11 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! 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: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 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: 0.6235440 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): -35.02100 9.725000 ymin,ymax (A): -0.9360000 41.05000 zmin,zma (A): -1.574000 55.51900 x,y,z range (A): 44.74600 41.98600 57.09300 scale (grids/A): 0.6235440 object centre (A): -12.64800 20.05700 26.97250 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 90.58179 90.09071 90.64242 assigned negative charge : -283.2443 centred at (gu) : 90.47384 90.26603 90.65388 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5147 nv = 96 ne = 84 npr = 39763 no. pairs analyzed = 39763 no. exposed pairs = 2436 no. arc points = 16976 no. surface atoms = 832 nbur = 1112 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 275 mr = 2822 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1672 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6270791E-08 -2.2767454E-08 midg,1,midg; midg,igrid,midg -9.8227311E-09 -2.9418864E-08 1,midg,midg; igrid,midg,midg -2.2176311E-08 -1.5242890E-08 gauss-seidel spectral radius is 0.9866237 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 14:21:12 rms-change max change #iterations 0.1117799 19.40678 at 10iterations 1.0523478E-02 1.641296 at 20iterations 9.7030471E-04 0.1643305 at 30iterations 8.9652363E-05 1.5026093E-02 at 40iterations 8.5296679E-06 1.3885498E-03 at 50iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 8.5296679E-06 1.3885498E-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) 4.460000 DelPhi exited at 14:21:17 4.463u 0.419s 0:06.02 80.8% 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 14:21:17 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! 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: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 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: 1.870632 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): -35.02100 9.725000 ymin,ymax (A): -0.9360000 41.05000 zmin,zma (A): -1.574000 55.51900 x,y,z range (A): 44.74600 41.98600 57.09300 scale (grids/A): 1.870632 object centre (A): -12.64800 20.05700 26.97250 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 91.74603 90.27235 91.92770 assigned negative charge : -283.2443 centred at (gu) : 91.42154 90.79834 91.96189 start vw surface at 0.1000000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 55895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 20566 mr = 38622 m= 3077 mr = 15512 m= 153 mr = 1883 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 23634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 13722 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) : 0.6235440 object centre at (A) : -12.64800 20.05700 26.97250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2913970E-02 -7.2552860E-02 midg,1,midg; midg,igrid,midg -1.9868137E-02 -4.4873696E-02 1,midg,midg; igrid,midg,midg -2.0197827E-02 -3.3317905E-02 gauss-seidel spectral radius is 0.9985093 estimated iterations to convergence 205 setup time was (sec) 0.8700000 now iterating at: 14:21:20 rms-change max change #iterations 3.377504 163.4965 at 10iterations 1.528233 56.92627 at 20iterations 0.6913416 28.09714 at 30iterations 0.3121125 11.81682 at 40iterations 0.1415900 4.999405 at 50iterations 6.3654065E-02 2.303778 at 60iterations 2.8937917E-02 1.056261 at 70iterations 1.3053086E-02 0.4713249 at 80iterations 5.9204223E-03 0.2124896 at 90iterations 2.6764239E-03 0.1048622 at 100iterations 1.2132876E-03 4.4136047E-02 at 110iterations 5.4739066E-04 1.9985199E-02 at 120iterations finished qdiffx linear iterations at : 14:21:29 total time elapsed so far: 10.42000 # loops : 120 mean,max change (kT/e) : 5.4739066E-04 1.9985199E-02 energy calculations done at 10.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 14:21:34 10.599u 0.455s 0:17.18 64.2% 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 14:21:35 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! 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: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 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: 2.805948 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): -35.02100 9.725000 ymin,ymax (A): -0.9360000 41.05000 zmin,zma (A): -1.574000 55.51900 x,y,z range (A): 44.74600 41.98600 57.09300 scale (grids/A): 2.805948 object centre (A): -12.64800 20.05700 26.97250 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 92.61907 90.40859 92.89150 assigned negative charge : -283.2443 centred at (gu) : 92.13247 91.19749 92.94286 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 129093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 66662 mr = 93346 m= 24096 mr = 55235 m= 5500 mr = 19630 m= 694 mr = 4089 m= 28 mr = 458 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 53300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 13951 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) : 1.870632 object centre at (A) : -12.64800 20.05700 26.97250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5994757 -1.098970 midg,1,midg; midg,igrid,midg -0.2302810 -0.5209354 1,midg,midg; igrid,midg,midg -0.2090932 -0.3608712 gauss-seidel spectral radius is 0.9992073 estimated iterations to convergence 280 setup time was (sec) 1.510000 now iterating at: 14:21:38 rms-change max change #iterations 7.971066 298.0875 at 10iterations 4.534173 119.6638 at 20iterations 2.566593 57.62413 at 30iterations 1.446820 34.78101 at 40iterations 0.8154002 18.03681 at 50iterations 0.4587151 10.13069 at 60iterations 0.2587681 5.550261 at 70iterations 0.1459189 3.522146 at 80iterations 8.2043953E-02 1.855042 at 90iterations 4.6174582E-02 1.052158 at 100iterations 2.5901897E-02 0.5374184 at 110iterations 1.4613285E-02 0.3218918 at 120iterations 8.2078781E-03 0.1738863 at 130iterations 4.6240361E-03 9.0953827E-02 at 140iterations 2.6042475E-03 5.5557251E-02 at 150iterations 1.4612239E-03 3.0426025E-02 at 160iterations 8.1997307E-04 1.8522263E-02 at 170iterations 4.6121783E-04 9.0403557E-03 at 180iterations finished qdiffx linear iterations at : 14:21:57 total time elapsed so far: 20.78000 # loops : 180 mean,max change (kT/e) : 4.6121783E-04 9.0403557E-03 energy calculations done at 20.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.94000 DelPhi exited at 14:22:06 20.949u 0.596s 0:30.74 70.0% 0+0k 0+0io 0pf+0w