Tue Oct 11 07:15:43 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 07:15:44 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3233 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5956464 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): 0.7770001 48.62500 ymin,ymax (A): -8.223000 49.08800 zmin,zma (A): 1.263000 61.03000 x,y,z range (A): 47.84800 57.31100 59.76700 scale (grids/A): 0.5956464 object centre (A): 24.70100 20.43250 31.14650 number of atom coordinates read : 3233 total number of charged atoms : 3081 net assigned charge : -1.099990 assigned positive charge : 487.9288 centred at (gu) : 89.61492 89.47443 90.77865 assigned negative charge : -489.0299 centred at (gu) : 89.56113 89.41571 90.70910 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7486 nv = 96 ne = 84 npr = 66759 no. pairs analyzed = 66759 no. exposed pairs = 3805 no. arc points = 25305 no. surface atoms = 1308 nbur = 1925 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 4331 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3300000 number of dielectric boundary points 3456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2633 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9558 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6916753E-09 2.8364551E-09 midg,1,midg; midg,igrid,midg -3.1398251E-09 1.7084510E-09 1,midg,midg; igrid,midg,midg -2.8193676E-09 1.5868545E-09 gauss-seidel spectral radius is 0.9854606 estimated iterations to convergence 68 setup time was (sec) 0.5600000 now iterating at: 07:15:44 rms-change max change #iterations 0.1226343 24.72997 at 10iterations 1.0905790E-02 1.613190 at 20iterations 1.3774376E-03 0.1970024 at 30iterations 3.2717688E-04 4.5701981E-02 at 40iterations 9.3814568E-05 1.3225555E-02 at 50iterations finished qdiffx linear iterations at : 07:15:47 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 9.3814568E-05 1.3225555E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 07:15:48 3.369u 0.201s 0:04.07 87.4% 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 Tue Oct 11 2011 at 07:15:48 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3233 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.786939 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): 0.7770001 48.62500 ymin,ymax (A): -8.223000 49.08800 zmin,zma (A): 1.263000 61.03000 x,y,z range (A): 47.84800 57.31100 59.76700 scale (grids/A): 1.786939 object centre (A): 24.70100 20.43250 31.14650 number of atom coordinates read : 3233 total number of charged atoms : 3081 net assigned charge : -1.099990 assigned positive charge : 487.9288 centred at (gu) : 88.84382 88.42263 92.33506 assigned negative charge : -489.0299 centred at (gu) : 88.68323 88.24688 92.12674 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25305 grid for indexing accessible points = 1.400000 m= 29947 mr = 59802 m= 3897 mr = 22607 m= 148 mr = 2399 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2224 time to turn everything in is 0.5800000 number of dielectric boundary points 32134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 24041 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) : 0.5956464 object centre at (A) : 24.70100 20.43250 31.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3065437E-02 2.1323655E-03 midg,1,midg; midg,igrid,midg -1.5656019E-02 4.3147721E-04 1,midg,midg; igrid,midg,midg -5.1099369E-03 1.6227550E-03 gauss-seidel spectral radius is 0.9985105 estimated iterations to convergence 205 setup time was (sec) 0.8600000 now iterating at: 07:15:49 rms-change max change #iterations 4.301026 193.0913 at 10iterations 1.949438 64.61582 at 20iterations 0.8861789 29.78112 at 30iterations 0.4010693 12.97655 at 40iterations 0.1827473 5.677677 at 50iterations 8.3118938E-02 2.771040 at 60iterations 3.7918046E-02 1.181440 at 70iterations 1.7219439E-02 0.5815887 at 80iterations 7.9188887E-03 0.2274971 at 90iterations 3.6660177E-03 0.1088867 at 100iterations 1.7361499E-03 5.4843903E-02 at 110iterations 8.4341806E-04 2.6961327E-02 at 120iterations finished qdiffx linear iterations at : 07:15:55 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 8.4341806E-04 2.6961327E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 07:15:56 7.608u 0.227s 0:08.14 96.0% 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 Tue Oct 11 2011 at 07:15:56 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3233 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.680409 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): 0.7770001 48.62500 ymin,ymax (A): -8.223000 49.08800 zmin,zma (A): 1.263000 61.03000 x,y,z range (A): 47.84800 57.31100 59.76700 scale (grids/A): 2.680409 object centre (A): 24.70100 20.43250 31.14650 number of atom coordinates read : 3233 total number of charged atoms : 3081 net assigned charge : -1.099990 assigned positive charge : 487.9288 centred at (gu) : 88.26558 87.63367 93.50239 assigned negative charge : -489.0299 centred at (gu) : 88.02468 87.37029 93.18999 start vw surface at 0.1800000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 192416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25305 grid for indexing accessible points = 1.400000 m= 99564 mr = 145074 m= 33516 mr = 82823 m= 6827 mr = 27044 m= 665 mr = 5143 m= 30 mr = 432 m= 0 mr = 11 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 7209 time to turn everything in is 1.460000 number of dielectric boundary points 72491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 24644 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) : 1.786939 object centre at (A) : 24.70100 20.43250 31.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3701115 -8.0723040E-02 midg,1,midg; midg,igrid,midg -0.3034260 -2.1564515E-02 1,midg,midg; igrid,midg,midg -3.8094200E-02 -8.4660221E-03 gauss-seidel spectral radius is 0.9992336 estimated iterations to convergence 285 setup time was (sec) 1.770000 now iterating at: 07:15:58 rms-change max change #iterations 10.35132 358.8582 at 10iterations 6.026137 136.6522 at 20iterations 3.481758 70.46738 at 30iterations 2.002164 41.89520 at 40iterations 1.149426 22.02101 at 50iterations 0.6584317 12.26839 at 60iterations 0.3764641 7.073726 at 70iterations 0.2156447 4.160509 at 80iterations 0.1228645 2.334305 at 90iterations 7.0245676E-02 1.333352 at 100iterations 4.0094655E-02 0.7007618 at 110iterations 2.2949455E-02 0.4351397 at 120iterations 1.3186762E-02 0.2313232 at 130iterations 7.6108673E-03 0.1347275 at 140iterations 4.4518239E-03 7.8272581E-02 at 150iterations 2.6526500E-03 5.1856995E-02 at 160iterations 1.6282417E-03 2.9714584E-02 at 170iterations 1.0411795E-03 1.9859076E-02 at 180iterations finished qdiffx linear iterations at : 07:16:08 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 1.0411795E-03 1.9859076E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 07:16:09 12.287u 0.220s 0:12.83 97.4% 0+0k 0+0io 0pf+0w