Wed Dec 21 14:22:33 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 21 2011 at 14:22:36 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: 263 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 : 267.4704 centred at (gu) : 90.40090 89.65702 90.81377 assigned negative charge : -289.4222 centred at (gu) : 90.32003 89.81100 90.82732 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 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 = 0.1100000 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 = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 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 0.3600000 number of grid points assigned charge 5987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3839449E-08 -2.1126018E-08 midg,1,midg; midg,igrid,midg -1.0549323E-08 -2.2842366E-08 1,midg,midg; igrid,midg,midg -1.9269203E-08 -1.4412405E-08 gauss-seidel spectral radius is 0.9864237 estimated iterations to convergence 70 setup time was (sec) 0.5700000 now iterating at: 14:22:37 rms-change max change #iterations 0.1160920 19.78673 at 10iterations 1.0489389E-02 1.964943 at 20iterations 9.6485013E-04 0.1755576 at 30iterations 8.7432447E-05 1.4863968E-02 at 40iterations 7.9204701E-06 1.3713837E-03 at 50iterations finished qdiffx linear iterations at : 14:22:44 total time elapsed so far: 7.660000 # loops : 50 mean,max change (kT/e) : 7.9204701E-06 1.3713837E-03 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 14:22:49 7.855u 0.424s 0:13.74 60.1% 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 14:22:51 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: 263 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 : 267.4704 centred at (gu) : 91.20313 88.97165 92.44170 assigned negative charge : -289.4222 centred at (gu) : 90.96025 89.43313 92.48192 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 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 = 0.2600000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.5100000 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 0.6500000 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 -3.7464231E-02 -6.4882323E-02 midg,1,midg; midg,igrid,midg -2.3598317E-02 -3.8124155E-02 1,midg,midg; igrid,midg,midg -2.3428813E-02 -3.1209299E-02 gauss-seidel spectral radius is 0.9984886 estimated iterations to convergence 204 setup time was (sec) 0.9000000 now iterating at: 14:22:53 rms-change max change #iterations 3.465026 168.7646 at 10iterations 1.557659 60.55733 at 20iterations 0.6982365 26.32026 at 30iterations 0.3170611 11.90056 at 40iterations 0.1417371 5.101642 at 50iterations 6.3929319E-02 2.220612 at 60iterations 2.8674131E-02 1.014351 at 70iterations 1.2951099E-02 0.4911175 at 80iterations 5.8072014E-03 0.2265244 at 90iterations 2.6211850E-03 8.9585781E-02 at 100iterations 1.1820309E-03 4.4585228E-02 at 110iterations 5.3220533E-04 2.0696163E-02 at 120iterations finished qdiffx linear iterations at : 14:23:11 total time elapsed so far: 19.02000 # loops : 120 mean,max change (kT/e) : 5.3220533E-04 2.0696163E-02 energy calculations done at 19.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.20000 DelPhi exited at 14:23:14 19.202u 0.549s 0:22.88 86.2% 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 14:23:15 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: 263 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 : 267.4704 centred at (gu) : 91.80461 88.45774 93.66260 assigned negative charge : -289.4222 centred at (gu) : 91.44034 89.14971 93.72293 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 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 = 0.7100000 no. cavity mid-points inaccessible to solvent = 861 time to turn everything in is 1.220000 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 1.410000 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 -0.5310931 -0.8846881 midg,1,midg; midg,igrid,midg -0.2785080 -0.4130794 1,midg,midg; igrid,midg,midg -0.2487466 -0.3367032 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 1.720000 now iterating at: 14:23:17 rms-change max change #iterations 8.117396 385.9301 at 10iterations 4.607663 130.7569 at 20iterations 2.603601 69.13016 at 30iterations 1.466310 32.15350 at 40iterations 0.8229531 18.11232 at 50iterations 0.4638516 10.75222 at 60iterations 0.2607347 5.347909 at 70iterations 0.1461441 3.108893 at 80iterations 8.1770502E-02 1.660538 at 90iterations 4.5905314E-02 1.033615 at 100iterations 2.5780557E-02 0.5192108 at 110iterations 1.4459147E-02 0.3293943 at 120iterations 8.1294198E-03 0.1799278 at 130iterations 4.5535527E-03 9.1859818E-02 at 140iterations 2.5509705E-03 4.9457550E-02 at 150iterations 1.4323504E-03 3.3666611E-02 at 160iterations 8.0447132E-04 1.6613007E-02 at 170iterations 4.5026280E-04 1.0601044E-02 at 180iterations finished qdiffx linear iterations at : 14:23:47 total time elapsed so far: 31.16000 # loops : 180 mean,max change (kT/e) : 4.5026280E-04 1.0601044E-02 energy calculations done at 31.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.33000 DelPhi exited at 14:23:48 31.336u 0.716s 0:32.58 98.3% 0+0k 0+0io 0pf+0w