Wed Dec 21 14:20:42 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 14:20:42 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6210530 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): -34.98300 10.45000 ymin,ymax (A): 1.138000 41.28500 zmin,zma (A): -1.719000 55.60300 x,y,z range (A): 45.43300 40.14700 57.32200 scale (grids/A): 0.6210530 object centre (A): -12.26650 21.21150 26.94200 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 263.6025 centred at (gu) : 90.29696 89.49623 90.60055 assigned negative charge : -285.5543 centred at (gu) : 90.20161 89.65058 90.61475 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5095 nv = 96 ne = 84 npr = 40471 no. pairs analyzed = 40471 no. exposed pairs = 2357 no. arc points = 16678 no. surface atoms = 802 nbur = 1156 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 235 mr = 2795 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1578 ## 114 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5953 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5481291E-08 -2.1610248E-08 midg,1,midg; midg,igrid,midg -1.1795032E-08 -2.3514747E-08 1,midg,midg; igrid,midg,midg -2.1721419E-08 -1.4397990E-08 gauss-seidel spectral radius is 0.9865165 estimated iterations to convergence 71 setup time was (sec) 0.3700000 now iterating at: 14:20:43 rms-change max change #iterations 0.1152469 21.19037 at 10iterations 1.0265006E-02 1.720098 at 20iterations 9.5057033E-04 0.1425228 at 30iterations 8.8770168E-05 1.5281677E-02 at 40iterations 8.1761027E-06 1.5039444E-03 at 50iterations finished qdiffx linear iterations at : 14:20:47 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 8.1761027E-06 1.5039444E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 14:20:48 4.437u 0.329s 0:05.87 80.9% 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 14:20:48 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.863159 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): -34.98300 10.45000 ymin,ymax (A): 1.138000 41.28500 zmin,zma (A): -1.719000 55.60300 x,y,z range (A): 45.43300 40.14700 57.32200 scale (grids/A): 1.863159 object centre (A): -12.26650 21.21150 26.94200 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 263.6025 centred at (gu) : 90.89111 88.48890 91.80205 assigned negative charge : -285.5543 centred at (gu) : 90.60498 88.95184 91.84447 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 55227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16678 grid for indexing accessible points = 1.400000 m= 19855 mr = 38340 m= 2641 mr = 14874 m= 128 mr = 1580 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 215 time to turn everything in is 0.2900000 number of dielectric boundary points 23019 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.3800000 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) : 0.6210530 object centre at (A) : -12.26650 21.21150 26.94200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8459083E-02 -6.5175511E-02 midg,1,midg; midg,igrid,midg -2.4591327E-02 -3.8139202E-02 1,midg,midg; igrid,midg,midg -2.5551427E-02 -3.0210566E-02 gauss-seidel spectral radius is 0.9984953 estimated iterations to convergence 204 setup time was (sec) 0.5700000 now iterating at: 14:20:49 rms-change max change #iterations 3.369131 172.3708 at 10iterations 1.524332 57.06165 at 20iterations 0.6865792 28.18189 at 30iterations 0.3095099 11.43570 at 40iterations 0.1399750 4.876801 at 50iterations 6.2868446E-02 2.212541 at 60iterations 2.8297311E-02 1.107377 at 70iterations 1.2745196E-02 0.4820156 at 80iterations 5.7578092E-03 0.2536478 at 90iterations 2.5942991E-03 9.1779709E-02 at 100iterations 1.1725364E-03 4.0962219E-02 at 110iterations 5.2981317E-04 2.0622253E-02 at 120iterations finished qdiffx linear iterations at : 14:21:00 total time elapsed so far: 11.30000 # loops : 120 mean,max change (kT/e) : 5.2981317E-04 2.0622253E-02 energy calculations done at 11.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 14:21:00 11.437u 0.308s 0:12.55 93.4% 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 21 2011 at 14:21:01 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.794738 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): -34.98300 10.45000 ymin,ymax (A): 1.138000 41.28500 zmin,zma (A): -1.719000 55.60300 x,y,z range (A): 45.43300 40.14700 57.32200 scale (grids/A): 2.794738 object centre (A): -12.26650 21.21150 26.94200 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 263.6025 centred at (gu) : 91.33673 87.73339 92.70331 assigned negative charge : -285.5543 centred at (gu) : 90.90746 88.42782 92.76661 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 127379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16678 grid for indexing accessible points = 1.400000 m= 65003 mr = 92452 m= 22283 mr = 53874 m= 4634 mr = 17957 m= 590 mr = 3454 m= 26 mr = 346 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 0.7300000 number of dielectric boundary points 51825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14062 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) : 1.863159 object centre at (A) : -12.26650 21.21150 26.94200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7220384 -1.077353 midg,1,midg; midg,igrid,midg -0.2936484 -0.4124513 1,midg,midg; igrid,midg,midg -0.2786536 -0.3246186 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 1.010000 now iterating at: 14:21:02 rms-change max change #iterations 8.067838 350.9188 at 10iterations 4.611054 112.5105 at 20iterations 2.606476 61.81456 at 30iterations 1.468384 30.40411 at 40iterations 0.8276810 17.06376 at 50iterations 0.4657191 9.700947 at 60iterations 0.2615176 5.336214 at 70iterations 0.1469923 3.021399 at 80iterations 8.2430623E-02 1.876221 at 90iterations 4.6272352E-02 0.9839706 at 100iterations 2.6017146E-02 0.5557747 at 110iterations 1.4571209E-02 0.2972527 at 120iterations 8.1919329E-03 0.1824117 at 130iterations 4.5879334E-03 9.3357086E-02 at 140iterations 2.5734641E-03 5.6108475E-02 at 150iterations 1.4438507E-03 3.0399323E-02 at 160iterations 8.1070774E-04 1.6976357E-02 at 170iterations 4.5452136E-04 8.8777542E-03 at 180iterations finished qdiffx linear iterations at : 14:21:17 total time elapsed so far: 16.24000 # loops : 180 mean,max change (kT/e) : 4.5452136E-04 8.8777542E-03 energy calculations done at 16.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.38000 DelPhi exited at 14:21:22 16.378u 0.343s 0:21.73 76.8% 0+0k 0+0io 0pf+0w