Sat Oct 8 15:22:21 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 15:22:21 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3311 !!! WARNING: SEP 61 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6006107 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): -61.77800 -2.505000 ymin,ymax (A): -25.57900 26.68600 zmin,zma (A): -10.37300 45.01200 x,y,z range (A): 59.27300 52.26500 55.38500 scale (grids/A): 0.6006107 object centre (A): -32.14150 0.5535002 17.31950 number of atom coordinates read : 3311 total number of charged atoms : 3162 net assigned charge : 4.025006 assigned positive charge : 496.7387 centred at (gu) : 92.07094 89.49473 90.48333 assigned negative charge : -492.7151 centred at (gu) : 92.14056 89.53625 90.40950 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7783 nv = 96 ne = 84 npr = 69039 no. pairs analyzed = 69039 no. exposed pairs = 3702 no. arc points = 25808 no. surface atoms = 1252 nbur = 2059 mkacc time = 0.1800000 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 = 1.456000 m= 335 mr = 4467 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3800000 number of dielectric boundary points 3614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2663 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5095041E-09 5.8444982E-09 midg,1,midg; midg,igrid,midg 4.1914707E-09 -1.3359236E-10 1,midg,midg; igrid,midg,midg 3.1696363E-09 -2.5018201E-09 gauss-seidel spectral radius is 0.9857027 estimated iterations to convergence 69 setup time was (sec) 0.6500000 now iterating at: 15:22:22 rms-change max change #iterations 0.1240223 16.16483 at 10iterations 1.0957124E-02 1.466388 at 20iterations 1.1118748E-03 0.1625595 at 30iterations 1.8584664E-04 3.4265518E-02 at 40iterations 4.8235732E-05 9.6244812E-03 at 50iterations finished qdiffx linear iterations at : 15:22:26 total time elapsed so far: 4.880000 # loops : 50 mean,max change (kT/e) : 4.8235732E-05 9.6244812E-03 energy calculations done at 4.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.030000 DelPhi exited at 15:22:27 5.038u 0.432s 0:05.81 93.9% 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 15:22:27 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3311 !!! WARNING: SEP 61 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.801832 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): -61.77800 -2.505000 ymin,ymax (A): -25.57900 26.68600 zmin,zma (A): -10.37300 45.01200 x,y,z range (A): 59.27300 52.26500 55.38500 scale (grids/A): 1.801832 object centre (A): -32.14150 0.5535002 17.31950 number of atom coordinates read : 3311 total number of charged atoms : 3162 net assigned charge : 4.025006 assigned positive charge : 496.7387 centred at (gu) : 96.21233 88.48311 91.44922 assigned negative charge : -492.7151 centred at (gu) : 96.42123 88.60854 91.22832 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25808 grid for indexing accessible points = 1.400000 m= 29383 mr = 61758 m= 3834 mr = 21726 m= 179 mr = 2344 m= 0 mr = 68 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2211 time to turn everything in is 0.6900000 number of dielectric boundary points 33321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 24664 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) : 0.6006107 object centre at (A) : -32.14150 0.5535002 17.31950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6110661E-03 -5.8723851E-03 midg,1,midg; midg,igrid,midg 1.4638497E-02 1.1068285E-02 1,midg,midg; igrid,midg,midg 2.7641041E-02 4.4191279E-03 gauss-seidel spectral radius is 0.9985371 estimated iterations to convergence 207 setup time was (sec) 1.000000 now iterating at: 15:22:28 rms-change max change #iterations 4.322520 171.0104 at 10iterations 1.964753 65.42662 at 20iterations 0.9003475 31.97236 at 30iterations 0.4104978 11.88209 at 40iterations 0.1873952 6.166195 at 50iterations 8.5513785E-02 2.968445 at 60iterations 3.9090320E-02 1.283863 at 70iterations 1.7879251E-02 0.5553741 at 80iterations 8.1909485E-03 0.2405958 at 90iterations 3.7757272E-03 0.1308498 at 100iterations 1.7481153E-03 5.4529190E-02 at 110iterations 8.1545865E-04 2.5739670E-02 at 120iterations finished qdiffx linear iterations at : 15:22:39 total time elapsed so far: 11.78000 # loops : 120 mean,max change (kT/e) : 8.1545865E-04 2.5739670E-02 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 15:22:40 11.951u 0.473s 0:12.72 97.6% 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 15:22:40 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3311 !!! WARNING: SEP 61 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.702748 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): -61.77800 -2.505000 ymin,ymax (A): -25.57900 26.68600 zmin,zma (A): -10.37300 45.01200 x,y,z range (A): 59.27300 52.26500 55.38500 scale (grids/A): 2.702748 object centre (A): -32.14150 0.5535002 17.31950 number of atom coordinates read : 3311 total number of charged atoms : 3162 net assigned charge : 4.025006 assigned positive charge : 496.7387 centred at (gu) : 99.31821 87.72465 92.17371 assigned negative charge : -492.7151 centred at (gu) : 99.63177 87.91255 91.84225 start vw surface at 0.1300000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 199285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25808 grid for indexing accessible points = 1.400000 m= 98917 mr = 149703 m= 32231 mr = 81617 m= 6578 mr = 25790 m= 768 mr = 4951 m= 39 mr = 517 m= 0 mr = 20 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 7610 time to turn everything in is 1.790000 number of dielectric boundary points 75220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 25292 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) : 1.801832 object centre at (A) : -32.14150 0.5535002 17.31950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7831648E-02 -0.1644348 midg,1,midg; midg,igrid,midg 5.9435569E-02 0.1403373 1,midg,midg; igrid,midg,midg 0.3304919 0.1284053 gauss-seidel spectral radius is 0.9992406 estimated iterations to convergence 286 setup time was (sec) 2.170000 now iterating at: 15:22:42 rms-change max change #iterations 10.32562 284.0186 at 10iterations 5.975703 145.8804 at 20iterations 3.431663 80.83010 at 30iterations 1.975075 37.88542 at 40iterations 1.132184 27.90341 at 50iterations 0.6482969 12.80573 at 60iterations 0.3710825 6.256365 at 70iterations 0.2124877 3.634836 at 80iterations 0.1214621 2.009704 at 90iterations 6.9445916E-02 1.298195 at 100iterations 3.9691266E-02 0.7120705 at 110iterations 2.2728151E-02 0.4373231 at 120iterations 1.3057493E-02 0.2296810 at 130iterations 7.5155739E-03 0.1384724 at 140iterations 4.3606022E-03 7.9466581E-02 at 150iterations 2.5604062E-03 4.9921036E-02 at 160iterations 1.5399111E-03 3.0891418E-02 at 170iterations 9.5767301E-04 2.2228241E-02 at 180iterations finished qdiffx linear iterations at : 15:23:01 total time elapsed so far: 20.37000 # loops : 180 mean,max change (kT/e) : 9.5767301E-04 2.2228241E-02 energy calculations done at 20.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.54000 DelPhi exited at 15:23:01 20.540u 0.533s 0:21.38 98.5% 0+0k 0+0io 0pf+0w