Sun Oct 9 11:53:15 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 Sun Oct 9 2011 at 11:53:15 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: HIR 200 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: 0.5636925 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): 60.12300 113.6320 ymin,ymax (A): -7.224000 55.93100 zmin,zma (A): -26.15100 30.11800 x,y,z range (A): 53.50901 63.15500 56.26900 scale (grids/A): 0.5636925 object centre (A): 86.87750 24.35350 1.983500 number of atom coordinates read : 2726 total number of charged atoms : 2583 net assigned charge : -2.985984 assigned positive charge : 395.4600 centred at (gu) : 89.92893 89.84081 90.02998 assigned negative charge : -398.4477 centred at (gu) : 90.00040 89.64272 90.13567 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6046 nv = 96 ne = 84 npr = 51753 no. pairs analyzed = 51753 no. exposed pairs = 4159 no. arc points = 30220 no. surface atoms = 1373 nbur = 1353 mkacc time = 0.1100000 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 = 1.512000 m= 286 mr = 2615 m= 0 mr = 8 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2885 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7470 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1800072E-10 -1.5810950E-09 midg,1,midg; midg,igrid,midg -2.7607885E-09 1.7619456E-09 1,midg,midg; igrid,midg,midg 4.5308032E-10 -1.1537428E-09 gauss-seidel spectral radius is 0.9837712 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 11:53:15 rms-change max change #iterations 7.9097651E-02 13.00962 at 10iterations 5.8100396E-03 1.134328 at 20iterations 4.7668687E-04 7.8615189E-02 at 30iterations 7.1448434E-05 1.4179230E-02 at 40iterations 1.6572629E-05 3.5343170E-03 at 50iterations finished qdiffx linear iterations at : 11:53:18 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.6572629E-05 3.5343170E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 11:53:18 3.134u 0.131s 0:03.54 92.0% 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 Sun Oct 9 2011 at 11:53:18 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: HIR 200 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: 1.691078 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): 60.12300 113.6320 ymin,ymax (A): -7.224000 55.93100 zmin,zma (A): -26.15100 30.11800 x,y,z range (A): 53.50901 63.15500 56.26900 scale (grids/A): 1.691078 object centre (A): 86.87750 24.35350 1.983500 number of atom coordinates read : 2726 total number of charged atoms : 2583 net assigned charge : -2.985984 assigned positive charge : 395.4600 centred at (gu) : 89.78584 89.52171 90.08886 assigned negative charge : -398.4477 centred at (gu) : 90.00105 88.92787 90.40678 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64990 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30220 grid for indexing accessible points = 1.400000 m= 19943 mr = 39440 m= 2595 mr = 12396 m= 101 mr = 1220 m= 0 mr = 10 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 34563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 20007 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) : 0.5636925 object centre at (A) : 86.87750 24.35350 1.983500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6652962E-04 -1.2214318E-02 midg,1,midg; midg,igrid,midg -2.3917485E-02 -1.0554379E-02 1,midg,midg; igrid,midg,midg 7.6818592E-03 -8.2355214E-04 gauss-seidel spectral radius is 0.9983366 estimated iterations to convergence 195 setup time was (sec) 0.7100000 now iterating at: 11:53:19 rms-change max change #iterations 3.409791 162.7157 at 10iterations 1.466194 53.20571 at 20iterations 0.6330095 26.93572 at 30iterations 0.2717725 10.30810 at 40iterations 0.1178168 5.150404 at 50iterations 5.0800271E-02 1.970676 at 60iterations 2.1918204E-02 0.7858400 at 70iterations 9.4954604E-03 0.3413353 at 80iterations 4.1161738E-03 0.1455994 at 90iterations 1.7911406E-03 6.8511486E-02 at 100iterations 7.8554137E-04 3.1845093E-02 at 110iterations 3.4796449E-04 1.4505386E-02 at 120iterations finished qdiffx linear iterations at : 11:53:25 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 3.4796449E-04 1.4505386E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 11:53:26 6.882u 0.186s 0:07.34 96.1% 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 Sun Oct 9 2011 at 11:53:26 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: HIR 200 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: 2.536616 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): 60.12300 113.6320 ymin,ymax (A): -7.224000 55.93100 zmin,zma (A): -26.15100 30.11800 x,y,z range (A): 53.50901 63.15500 56.26900 scale (grids/A): 2.536616 object centre (A): 86.87750 24.35350 1.983500 number of atom coordinates read : 2726 total number of charged atoms : 2583 net assigned charge : -2.985984 assigned positive charge : 395.4600 centred at (gu) : 89.67845 89.28230 90.13326 assigned negative charge : -398.4477 centred at (gu) : 90.00137 88.39176 90.61003 start vw surface at 0.1600000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 150728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30220 grid for indexing accessible points = 1.400000 m= 65975 mr = 98483 m= 20569 mr = 48058 m= 4122 mr = 14461 m= 388 mr = 2617 m= 5 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 78012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 20654 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) : 1.691078 object centre at (A) : 86.87750 24.35350 1.983500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8602494E-02 -0.1660225 midg,1,midg; midg,igrid,midg -0.2955639 -0.1479725 1,midg,midg; igrid,midg,midg 0.1383367 -2.4985470E-02 gauss-seidel spectral radius is 0.9992043 estimated iterations to convergence 280 setup time was (sec) 1.380000 now iterating at: 11:53:27 rms-change max change #iterations 8.807162 269.2417 at 10iterations 5.160661 138.5894 at 20iterations 2.999925 98.10482 at 30iterations 1.726797 44.75077 at 40iterations 0.9932031 26.68077 at 50iterations 0.5666128 13.46673 at 60iterations 0.3233391 6.527738 at 70iterations 0.1834427 3.785915 at 80iterations 0.1038432 2.377838 at 90iterations 5.8780130E-02 1.348671 at 100iterations 3.3371191E-02 0.7239380 at 110iterations 1.8819042E-02 0.4063110 at 120iterations 1.0596901E-02 0.2245631 at 130iterations 5.9911883E-03 0.1220474 at 140iterations 3.3821058E-03 7.1527481E-02 at 150iterations 1.9105431E-03 4.0203720E-02 at 160iterations 1.0777750E-03 2.3891449E-02 at 170iterations 6.1032834E-04 1.1688232E-02 at 180iterations finished qdiffx linear iterations at : 11:53:37 total time elapsed so far: 10.82000 # loops : 180 mean,max change (kT/e) : 6.1032834E-04 1.1688232E-02 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.00000 DelPhi exited at 11:53:37 11.002u 0.152s 0:11.50 96.9% 0+0k 0+0io 0pf+0w