Tue Oct 11 06:11:57 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 06:11:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2024 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7233126 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): -19.43100 23.86100 ymin,ymax (A): 0.7210001 39.09500 zmin,zma (A): 20.46000 69.67800 x,y,z range (A): 43.29200 38.37400 49.21800 scale (grids/A): 0.7233126 object centre (A): 2.215000 19.90800 45.06900 number of atom coordinates read : 2024 total number of charged atoms : 1899 net assigned charge : 7.039010 assigned positive charge : 308.7841 centred at (gu) : 89.94715 90.90858 89.82999 assigned negative charge : -301.7451 centred at (gu) : 89.74934 90.89371 89.80268 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7309 nv = 96 ne = 84 npr = 40754 no. pairs analyzed = 40754 no. exposed pairs = 2479 no. arc points = 16798 no. surface atoms = 845 nbur = 1179 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 4224 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1555 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7853 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9455439E-08 1.0101869E-07 midg,1,midg; midg,igrid,midg 6.4275014E-08 1.1357302E-07 1,midg,midg; igrid,midg,midg -5.1053021E-08 2.1482487E-07 gauss-seidel spectral radius is 0.9900266 estimated iterations to convergence 81 setup time was (sec) 0.6500000 now iterating at: 06:11:58 rms-change max change #iterations 0.2146940 27.98418 at 10iterations 2.8078619E-02 3.313273 at 20iterations 3.9038961E-03 0.4771118 at 30iterations 6.3127402E-04 7.8971863E-02 at 40iterations 1.4311688E-04 1.7055511E-02 at 50iterations finished qdiffx linear iterations at : 06:12:02 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 1.4311688E-04 1.7055511E-02 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 06:12:02 4.672u 0.432s 0:05.50 92.7% 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 Tue Oct 11 2011 at 06:12:02 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2024 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.169938 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): -19.43100 23.86100 ymin,ymax (A): 0.7210001 39.09500 zmin,zma (A): 20.46000 69.67800 x,y,z range (A): 43.29200 38.37400 49.21800 scale (grids/A): 2.169938 object centre (A): 2.215000 19.90800 45.06900 number of atom coordinates read : 2024 total number of charged atoms : 1899 net assigned charge : 7.039010 assigned positive charge : 308.7841 centred at (gu) : 89.84153 92.72604 89.48975 assigned negative charge : -301.7451 centred at (gu) : 89.24809 92.68118 89.40809 start vw surface at 0.1400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 76616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16798 grid for indexing accessible points = 1.400000 m= 32165 mr = 54736 m= 6760 mr = 24699 m= 643 mr = 4579 m= 15 mr = 343 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 31842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 15095 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) : 0.7233126 object centre at (A) : 2.215000 19.90800 45.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0261000E-02 5.3274684E-02 midg,1,midg; midg,igrid,midg 5.4767728E-03 3.5300769E-02 1,midg,midg; igrid,midg,midg 8.0985250E-03 4.9839564E-02 gauss-seidel spectral radius is 0.9988688 estimated iterations to convergence 235 setup time was (sec) 1.160000 now iterating at: 06:12:04 rms-change max change #iterations 4.729972 200.3763 at 10iterations 2.360421 74.13647 at 20iterations 1.195104 39.34520 at 30iterations 0.5990562 18.41912 at 40iterations 0.3004976 9.625082 at 50iterations 0.1521666 4.667202 at 60iterations 7.6252565E-02 2.167480 at 70iterations 3.8409404E-02 1.190018 at 80iterations 1.9400431E-02 0.5571575 at 90iterations 9.8182196E-03 0.2869492 at 100iterations 4.9880408E-03 0.1465378 at 110iterations 2.5621119E-03 7.5899124E-02 at 120iterations finished qdiffx linear iterations at : 06:12:14 total time elapsed so far: 10.87000 # loops : 120 mean,max change (kT/e) : 2.5621119E-03 7.5899124E-02 energy calculations done at 10.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 06:12:15 11.092u 0.477s 0:12.40 93.2% 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 06:12:15 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2024 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.254907 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): -19.43100 23.86100 ymin,ymax (A): 0.7210001 39.09500 zmin,zma (A): 20.46000 69.67800 x,y,z range (A): 43.29200 38.37400 49.21800 scale (grids/A): 3.254907 object centre (A): 2.215000 19.90800 45.06900 number of atom coordinates read : 2024 total number of charged atoms : 1899 net assigned charge : 7.039010 assigned positive charge : 308.7841 centred at (gu) : 89.76228 94.08913 89.23463 assigned negative charge : -301.7451 centred at (gu) : 88.87219 94.02171 89.11219 start vw surface at 0.1400000 fill in re-entrant regions at 1.010000 boundary points on vw surface= 176299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16798 grid for indexing accessible points = 1.400000 m= 98770 mr = 131685 m= 42540 mr = 82656 m= 12945 mr = 35177 m= 2622 mr = 10128 m= 313 mr = 1919 m= 5 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.550000 number of dielectric boundary points 71725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.700000 number of grid points assigned charge 15188 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) : 2.169938 object centre at (A) : 2.215000 19.90800 45.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8230008 0.4120298 midg,1,midg; midg,igrid,midg 7.6746582E-03 0.2642447 1,midg,midg; igrid,midg,midg 0.1384033 0.3807794 gauss-seidel spectral radius is 0.9993030 estimated iterations to convergence 299 setup time was (sec) 2.920000 now iterating at: 06:12:18 rms-change max change #iterations 10.46149 321.8008 at 10iterations 6.210752 130.4230 at 20iterations 3.687494 76.17479 at 30iterations 2.182939 44.48746 at 40iterations 1.288760 24.71766 at 50iterations 0.7590142 14.33989 at 60iterations 0.4480824 7.775864 at 70iterations 0.2633557 4.897667 at 80iterations 0.1553096 2.694380 at 90iterations 9.1235526E-02 1.637966 at 100iterations 5.3697996E-02 0.9158983 at 110iterations 3.1789538E-02 0.5472107 at 120iterations 1.8911421E-02 0.3377266 at 130iterations 1.1457299E-02 0.1994133 at 140iterations 7.0957565E-03 0.1319237 at 150iterations 4.5761061E-03 8.3709717E-02 at 160iterations 3.1135071E-03 5.9326172E-02 at 170iterations 2.2551192E-03 3.9218903E-02 at 180iterations finished qdiffx linear iterations at : 06:12:35 total time elapsed so far: 20.15000 # loops : 180 mean,max change (kT/e) : 2.2551192E-03 3.9218903E-02 energy calculations done at 20.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.37000 DelPhi exited at 06:12:36 20.374u 0.517s 0:21.49 97.1% 0+0k 0+0io 0pf+0w