Sat Oct 8 14:33:28 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 Sat Oct 8 2011 at 14:33:28 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6156507 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): -13.78700 35.52500 ymin,ymax (A): -12.18000 45.64500 zmin,zma (A): -39.92800 12.64000 x,y,z range (A): 49.31200 57.82500 52.56800 scale (grids/A): 0.6156507 object centre (A): 10.86900 16.73250 -13.64400 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -0.9859939 assigned positive charge : 456.3106 centred at (gu) : 91.53741 91.65978 91.04993 assigned negative charge : -457.2973 centred at (gu) : 91.58285 91.54393 91.11935 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7476 nv = 96 ne = 84 npr = 64087 no. pairs analyzed = 64087 no. exposed pairs = 3465 no. arc points = 24030 no. surface atoms = 1178 nbur = 1856 mkacc time = 0.2600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 4320 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.5200000 number of dielectric boundary points 3490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2379 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 9369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1512435E-09 -6.9888224E-09 midg,1,midg; midg,igrid,midg -6.0516014E-09 1.0406004E-08 1,midg,midg; igrid,midg,midg 1.6752395E-09 -5.4478471E-09 gauss-seidel spectral radius is 0.9863674 estimated iterations to convergence 70 setup time was (sec) 0.8200000 now iterating at: 14:33:29 rms-change max change #iterations 0.1345454 17.84738 at 10iterations 1.2707924E-02 1.701004 at 20iterations 1.2037699E-03 0.1663389 at 30iterations 1.3747298E-04 1.7762661E-02 at 40iterations 1.9690046E-05 2.9182434E-03 at 50iterations finished qdiffx linear iterations at : 14:33:33 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 1.9690046E-05 2.9182434E-03 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 14:33:33 5.007u 0.449s 0:05.73 94.9% 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 Sat Oct 8 2011 at 14:33:33 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.846952 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): -13.78700 35.52500 ymin,ymax (A): -12.18000 45.64500 zmin,zma (A): -39.92800 12.64000 x,y,z range (A): 49.31200 57.82500 52.56800 scale (grids/A): 1.846952 object centre (A): 10.86900 16.73250 -13.64400 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -0.9859939 assigned positive charge : 456.3106 centred at (gu) : 94.61149 94.97874 93.14927 assigned negative charge : -457.2973 centred at (gu) : 94.74826 94.63158 93.35786 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 82224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24030 grid for indexing accessible points = 1.400000 m= 28685 mr = 59199 m= 3918 mr = 21319 m= 152 mr = 2346 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 768 time to turn everything in is 0.8400000 number of dielectric boundary points 32082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 22655 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) : 0.6156507 object centre at (A) : 10.86900 16.73250 -13.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5755735E-02 4.8126965E-03 midg,1,midg; midg,igrid,midg -3.2814641E-02 3.9139349E-02 1,midg,midg; igrid,midg,midg 7.8547867E-03 -1.0391262E-02 gauss-seidel spectral radius is 0.9985845 estimated iterations to convergence 211 setup time was (sec) 1.200000 now iterating at: 14:33:35 rms-change max change #iterations 4.447614 209.8114 at 10iterations 2.050254 70.21644 at 20iterations 0.9532169 29.15000 at 30iterations 0.4396785 12.76736 at 40iterations 0.2044343 6.857605 at 50iterations 9.4325133E-02 3.019406 at 60iterations 4.3687563E-02 1.440826 at 70iterations 2.0210583E-02 0.5924759 at 80iterations 9.3560284E-03 0.2985744 at 90iterations 4.3386980E-03 0.1340857 at 100iterations 2.0210524E-03 6.8453789E-02 at 110iterations 9.3803491E-04 2.8044224E-02 at 120iterations finished qdiffx linear iterations at : 14:33:45 total time elapsed so far: 11.37000 # loops : 120 mean,max change (kT/e) : 9.3803491E-04 2.8044224E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 14:33:46 11.603u 0.492s 0:12.37 97.7% 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 Sat Oct 8 2011 at 14:33:46 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.770428 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): -13.78700 35.52500 ymin,ymax (A): -12.18000 45.64500 zmin,zma (A): -39.92800 12.64000 x,y,z range (A): 49.31200 57.82500 52.56800 scale (grids/A): 2.770428 object centre (A): 10.86900 16.73250 -13.64400 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -0.9859939 assigned positive charge : 456.3106 centred at (gu) : 96.91694 97.46792 94.72372 assigned negative charge : -457.2973 centred at (gu) : 97.12234 96.94733 95.03675 start vw surface at 0.1700000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 190776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24030 grid for indexing accessible points = 1.400000 m= 95461 mr = 143329 m= 32038 mr = 79029 m= 6752 mr = 25649 m= 757 mr = 4975 m= 23 mr = 439 m= 0 mr = 4 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 2618 time to turn everything in is 2.160000 number of dielectric boundary points 72382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 23095 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) : 1.846952 object centre at (A) : 10.86900 16.73250 -13.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1726716 0.2198144 midg,1,midg; midg,igrid,midg -0.3189226 0.5289806 1,midg,midg; igrid,midg,midg 0.1045955 -8.2580723E-02 gauss-seidel spectral radius is 0.9992459 estimated iterations to convergence 287 setup time was (sec) 2.550000 now iterating at: 14:33:49 rms-change max change #iterations 10.38969 351.7779 at 10iterations 6.037122 126.2100 at 20iterations 3.476059 68.47866 at 30iterations 1.998624 39.49353 at 40iterations 1.145094 23.86355 at 50iterations 0.6568757 11.58881 at 60iterations 0.3761602 6.996891 at 70iterations 0.2162507 4.229477 at 80iterations 0.1236097 2.417187 at 90iterations 7.0776395E-02 1.331135 at 100iterations 4.0366668E-02 0.6964226 at 110iterations 2.3115588E-02 0.3925443 at 120iterations 1.3201529E-02 0.2239303 at 130iterations 7.5864112E-03 0.1279411 at 140iterations 4.3333331E-03 7.2812080E-02 at 150iterations 2.4872271E-03 4.0344238E-02 at 160iterations 1.4293474E-03 2.4803162E-02 at 170iterations 8.2399242E-04 1.3202667E-02 at 180iterations finished qdiffx linear iterations at : 14:34:06 total time elapsed so far: 19.81000 # loops : 180 mean,max change (kT/e) : 8.2399242E-04 1.3202667E-02 energy calculations done at 19.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.04000 DelPhi exited at 14:34:07 20.045u 0.543s 0:20.89 98.5% 0+0k 0+0io 0pf+0w