Tue Oct 11 06:56:10 PDT 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 Tue Oct 11 2011 at 06:56:10 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5582475 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): -18.48000 45.29100 ymin,ymax (A): 21.48800 78.71800 zmin,zma (A): -72.17300 -23.75100 x,y,z range (A): 63.77100 57.23000 48.42200 scale (grids/A): 0.5582475 object centre (A): 13.40550 50.10300 -47.96200 number of atom coordinates read : 2859 total number of charged atoms : 2719 net assigned charge : 1.039007 assigned positive charge : 415.1137 centred at (gu) : 89.43056 89.72070 89.79720 assigned negative charge : -414.0753 centred at (gu) : 89.46745 89.76920 89.76517 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5790 nv = 96 ne = 84 npr = 58183 no. pairs analyzed = 58183 no. exposed pairs = 3697 no. arc points = 25661 no. surface atoms = 1260 nbur = 1599 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 312 mr = 2955 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2548 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7451 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2236898E-10 3.9036716E-10 midg,1,midg; midg,igrid,midg 6.0856015E-10 -3.4750874E-10 1,midg,midg; igrid,midg,midg 5.2535215E-10 -2.2441617E-10 gauss-seidel spectral radius is 0.9834443 estimated iterations to convergence 64 setup time was (sec) 0.6400000 now iterating at: 06:56:11 rms-change max change #iterations 8.0304235E-02 14.18585 at 10iterations 5.6653488E-03 0.9251366 at 20iterations 4.2001493E-04 5.9495687E-02 at 30iterations 4.4452478E-05 8.8462830E-03 at 40iterations 9.5772639E-06 2.0756721E-03 at 50iterations finished qdiffx linear iterations at : 06:56:14 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 9.5772639E-06 2.0756721E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 06:56:15 4.102u 0.261s 0:04.78 91.2% 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 Tue Oct 11 2011 at 06:56:15 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.674742 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): -18.48000 45.29100 ymin,ymax (A): 21.48800 78.71800 zmin,zma (A): -72.17300 -23.75100 x,y,z range (A): 63.77100 57.23000 48.42200 scale (grids/A): 1.674742 object centre (A): 13.40550 50.10300 -47.96200 number of atom coordinates read : 2859 total number of charged atoms : 2719 net assigned charge : 1.039007 assigned positive charge : 415.1137 centred at (gu) : 88.29140 89.16152 89.39070 assigned negative charge : -414.0753 centred at (gu) : 88.40211 89.30743 89.29497 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 63373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25661 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21455 mr = 42183 m= 2838 mr = 15135 m= 100 mr = 1636 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 28793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20929 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) : 0.5582475 object centre at (A) : 13.40550 50.10300 -47.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4695072E-03 1.0510406E-02 midg,1,midg; midg,igrid,midg -5.3655491E-03 1.1603417E-02 1,midg,midg; igrid,midg,midg 5.6123342E-03 -1.8337609E-02 gauss-seidel spectral radius is 0.9982736 estimated iterations to convergence 191 setup time was (sec) 0.9100000 now iterating at: 06:56:16 rms-change max change #iterations 3.374061 176.9080 at 10iterations 1.431225 63.04385 at 20iterations 0.6110997 22.56557 at 30iterations 0.2596733 10.35987 at 40iterations 0.1109104 3.722076 at 50iterations 4.7169577E-02 1.741428 at 60iterations 2.0099528E-02 0.7196693 at 70iterations 8.5612927E-03 0.3601913 at 80iterations 3.6525815E-03 0.1264014 at 90iterations 1.5551043E-03 5.5740058E-02 at 100iterations 6.6355715E-04 2.2720337E-02 at 110iterations 2.8450289E-04 1.0297775E-02 at 120iterations finished qdiffx linear iterations at : 06:56:24 total time elapsed so far: 9.080000 # loops : 120 mean,max change (kT/e) : 2.8450289E-04 1.0297775E-02 energy calculations done at 9.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.250000 DelPhi exited at 06:56:25 9.251u 0.286s 0:09.81 97.1% 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 Tue Oct 11 2011 at 06:56:25 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.512114 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): -18.48000 45.29100 ymin,ymax (A): 21.48800 78.71800 zmin,zma (A): -72.17300 -23.75100 x,y,z range (A): 63.77100 57.23000 48.42200 scale (grids/A): 2.512114 object centre (A): 13.40550 50.10300 -47.96200 number of atom coordinates read : 2859 total number of charged atoms : 2719 net assigned charge : 1.039007 assigned positive charge : 415.1137 centred at (gu) : 87.43692 88.74209 89.08591 assigned negative charge : -414.0753 centred at (gu) : 87.60297 88.96103 88.94247 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 146713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25661 grid for indexing accessible points = 1.400000 m= 70599 mr = 103177 m= 23918 mr = 55887 m= 4959 mr = 18778 m= 448 mr = 3642 m= 5 mr = 229 m= 0 mr = 2 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 64927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 21739 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) : 1.674742 object centre at (A) : 13.40550 50.10300 -47.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0894541E-02 0.1875027 midg,1,midg; midg,igrid,midg -8.4559023E-02 0.1881139 1,midg,midg; igrid,midg,midg 3.7988331E-02 -0.4941261 gauss-seidel spectral radius is 0.9991696 estimated iterations to convergence 274 setup time was (sec) 1.760000 now iterating at: 06:56:27 rms-change max change #iterations 8.660109 300.1517 at 10iterations 4.924473 132.4824 at 20iterations 2.783719 61.96359 at 30iterations 1.566764 35.23888 at 40iterations 0.8812394 17.92467 at 50iterations 0.4918270 10.62995 at 60iterations 0.2753718 5.568527 at 70iterations 0.1535795 3.090295 at 80iterations 8.5319497E-02 1.790274 at 90iterations 4.7648828E-02 1.013580 at 100iterations 2.6521923E-02 0.5566406 at 110iterations 1.4692149E-02 0.2823620 at 120iterations 8.1701856E-03 0.1771622 at 130iterations 4.5519900E-03 8.4049225E-02 at 140iterations 2.5243380E-03 4.9327850E-02 at 150iterations 1.4016102E-03 3.0822754E-02 at 160iterations 7.7944237E-04 1.4690399E-02 at 170iterations 4.3269177E-04 8.2836151E-03 at 180iterations finished qdiffx linear iterations at : 06:56:40 total time elapsed so far: 15.07000 # loops : 180 mean,max change (kT/e) : 4.3269177E-04 8.2836151E-03 energy calculations done at 15.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.25000 DelPhi exited at 06:56:41 15.253u 0.315s 0:15.95 97.5% 0+0k 0+0io 0pf+0w