Wed Dec 28 11:02:10 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 11:02:10 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! 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: ARG 14 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! 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 106 has a net charge of -0.6880 !!! WARNING: GLN 111 has a net charge of -0.6880 !!! WARNING: ARG 112 has a net charge of -0.4460 !!! WARNING: GLN 122 has a net charge of -0.6880 !!! WARNING: ARG 145 has a net charge of -0.4460 !!! WARNING: ARG 161 has a net charge of -0.4460 !!! WARNING: GLN 162 has a net charge of -0.6880 !!! WARNING: GLN 165 has a net charge of -0.6880 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 192 has a net charge of -0.6880 !!! WARNING: GLN 196 has a net charge of -0.6880 !!! WARNING: ASN 202 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: 0.5952381 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): -24.50900 35.29900 ymin,ymax (A): -19.21700 20.72400 zmin,zma (A): -2.788000 39.86600 x,y,z range (A): 59.80800 39.94100 42.65400 scale (grids/A): 0.5952381 object centre (A): 5.395000 0.7535000 18.53900 number of atom coordinates read : 1997 total number of charged atoms : 1795 net assigned charge : -21.64003 assigned positive charge : 273.3734 centred at (gu) : 89.68138 90.43860 90.11588 assigned negative charge : -295.0132 centred at (gu) : 89.72914 90.57885 90.22411 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4862 nv = 96 ne = 84 npr = 40228 no. pairs analyzed = 40228 no. exposed pairs = 2437 no. arc points = 17224 no. surface atoms = 830 nbur = 1167 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 216 mr = 2725 m= 0 mr = 16 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1628 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 5687 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2235358E-09 -1.0809448E-08 midg,1,midg; midg,igrid,midg -4.2016306E-09 -1.2496488E-08 1,midg,midg; igrid,midg,midg -7.2665496E-09 -8.4403098E-09 gauss-seidel spectral radius is 0.9853457 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 11:02:11 rms-change max change #iterations 9.4588690E-02 17.86513 at 10iterations 7.8570424E-03 1.425766 at 20iterations 6.5662817E-04 0.1089096 at 30iterations 5.5070592E-05 8.7013245E-03 at 40iterations 4.5575903E-06 7.0953369E-04 at 50iterations finished qdiffx linear iterations at : 11:02:15 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 4.5575903E-06 7.0953369E-04 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 11:02:17 4.413u 0.394s 0:07.44 64.5% 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 Wed Dec 28 2011 at 11:02:18 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! 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: ARG 14 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! 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 106 has a net charge of -0.6880 !!! WARNING: GLN 111 has a net charge of -0.6880 !!! WARNING: ARG 112 has a net charge of -0.4460 !!! WARNING: GLN 122 has a net charge of -0.6880 !!! WARNING: ARG 145 has a net charge of -0.4460 !!! WARNING: ARG 161 has a net charge of -0.4460 !!! WARNING: GLN 162 has a net charge of -0.6880 !!! WARNING: GLN 165 has a net charge of -0.6880 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 192 has a net charge of -0.6880 !!! WARNING: GLN 196 has a net charge of -0.6880 !!! WARNING: ASN 202 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: 1.785714 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): -24.50900 35.29900 ymin,ymax (A): -19.21700 20.72400 zmin,zma (A): -2.788000 39.86600 x,y,z range (A): 59.80800 39.94100 42.65400 scale (grids/A): 1.785714 object centre (A): 5.395000 0.7535000 18.53900 number of atom coordinates read : 1997 total number of charged atoms : 1795 net assigned charge : -21.64003 assigned positive charge : 273.3734 centred at (gu) : 89.04436 91.31583 90.34766 assigned negative charge : -295.0132 centred at (gu) : 89.18764 91.73669 90.67239 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 52692 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17224 grid for indexing accessible points = 1.400000 m= 18968 mr = 36551 m= 2378 mr = 14446 m= 74 mr = 1403 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1158 time to turn everything in is 0.4200000 number of dielectric boundary points 21690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 13991 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) : 0.5952381 object centre at (A) : 5.395000 0.7535000 18.53900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1161650E-03 -2.6452508E-02 midg,1,midg; midg,igrid,midg -1.1749612E-02 -3.0839460E-02 1,midg,midg; igrid,midg,midg -1.6384505E-02 -2.9924108E-02 gauss-seidel spectral radius is 0.9983767 estimated iterations to convergence 197 setup time was (sec) 0.7700000 now iterating at: 11:02:20 rms-change max change #iterations 3.182920 146.7837 at 10iterations 1.394564 56.67612 at 20iterations 0.6106537 27.33211 at 30iterations 0.2657453 10.51526 at 40iterations 0.1161002 4.983268 at 50iterations 5.0551284E-02 1.862984 at 60iterations 2.2244647E-02 0.8902931 at 70iterations 9.7045526E-03 0.3796768 at 80iterations 4.2250091E-03 0.1665535 at 90iterations 1.8510190E-03 7.3623657E-02 at 100iterations 8.1010471E-04 3.2459259E-02 at 110iterations 3.5462179E-04 1.4480591E-02 at 120iterations finished qdiffx linear iterations at : 11:02:29 total time elapsed so far: 10.19000 # loops : 120 mean,max change (kT/e) : 3.5462179E-04 1.4480591E-02 energy calculations done at 10.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.36000 DelPhi exited at 11:02:30 10.369u 0.438s 0:11.94 90.3% 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 11:02:31 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1997 !!! 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: ARG 14 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! 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 106 has a net charge of -0.6880 !!! WARNING: GLN 111 has a net charge of -0.6880 !!! WARNING: ARG 112 has a net charge of -0.4460 !!! WARNING: GLN 122 has a net charge of -0.6880 !!! WARNING: ARG 145 has a net charge of -0.4460 !!! WARNING: ARG 161 has a net charge of -0.4460 !!! WARNING: GLN 162 has a net charge of -0.6880 !!! WARNING: GLN 165 has a net charge of -0.6880 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 192 has a net charge of -0.6880 !!! WARNING: GLN 196 has a net charge of -0.6880 !!! WARNING: ASN 202 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: 2.678571 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): -24.50900 35.29900 ymin,ymax (A): -19.21700 20.72400 zmin,zma (A): -2.788000 39.86600 x,y,z range (A): 59.80800 39.94100 42.65400 scale (grids/A): 2.678571 object centre (A): 5.395000 0.7535000 18.53900 number of atom coordinates read : 1997 total number of charged atoms : 1795 net assigned charge : -21.64003 assigned positive charge : 273.3734 centred at (gu) : 88.56677 91.97388 90.52169 assigned negative charge : -295.0132 centred at (gu) : 88.78156 92.60502 91.00853 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 121315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17224 grid for indexing accessible points = 1.400000 m= 62458 mr = 87803 m= 21406 mr = 52273 m= 4087 mr = 17492 m= 407 mr = 2993 m= 11 mr = 242 m= 0 mr = 3 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 3949 time to turn everything in is 1.080000 number of dielectric boundary points 48878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14347 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) : 1.785714 object centre at (A) : 5.395000 0.7535000 18.53900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0503822E-02 -0.2926897 midg,1,midg; midg,igrid,midg -0.1366885 -0.3468801 1,midg,midg; igrid,midg,midg -8.1280760E-02 -0.3997760 gauss-seidel spectral radius is 0.9991667 estimated iterations to convergence 274 setup time was (sec) 1.400000 now iterating at: 11:02:33 rms-change max change #iterations 7.660679 306.5020 at 10iterations 4.286962 119.6800 at 20iterations 2.381864 61.01543 at 30iterations 1.324245 33.17979 at 40iterations 0.7339929 17.46018 at 50iterations 0.4075901 8.963278 at 60iterations 0.2260444 5.021149 at 70iterations 0.1248557 2.647208 at 80iterations 6.9075853E-02 1.629401 at 90iterations 3.8305264E-02 0.8153687 at 100iterations 2.1226536E-02 0.5036640 at 110iterations 1.1715766E-02 0.2489414 at 120iterations 6.5179211E-03 0.1518021 at 130iterations 3.6020877E-03 8.2115173E-02 at 140iterations 1.9963724E-03 4.2640686E-02 at 150iterations 1.1044489E-03 2.2973537E-02 at 160iterations 6.1329408E-04 1.4023781E-02 at 170iterations 3.3855121E-04 8.3141327E-03 at 180iterations finished qdiffx linear iterations at : 11:02:48 total time elapsed so far: 16.23000 # loops : 180 mean,max change (kT/e) : 3.3855121E-04 8.3141327E-03 energy calculations done at 16.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.40000 DelPhi exited at 11:02:49 16.401u 0.467s 0:18.02 93.5% 0+0k 0+0io 0pf+0w