Sat Oct 8 14:11:16 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 14:11:16 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 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: 0.6395171 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): -11.33300 44.33400 ymin,ymax (A): 10.69000 54.73700 zmin,zma (A): 41.43200 94.31700 x,y,z range (A): 55.66700 44.04700 52.88500 scale (grids/A): 0.6395171 object centre (A): 16.50050 32.71350 67.87450 number of atom coordinates read : 2925 total number of charged atoms : 2781 net assigned charge : -0.9859930 assigned positive charge : 438.0637 centred at (gu) : 88.88476 89.56994 90.21225 assigned negative charge : -439.0505 centred at (gu) : 88.85823 89.49714 90.18118 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8063 nv = 96 ne = 84 npr = 61144 no. pairs analyzed = 61144 no. exposed pairs = 3375 no. arc points = 23342 no. surface atoms = 1158 nbur = 1767 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 4744 m= 4 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2246 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9678 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1455729E-09 2.8285896E-09 midg,1,midg; midg,igrid,midg -1.1943479E-08 7.3367801E-09 1,midg,midg; igrid,midg,midg -6.0997021E-09 1.6420255E-09 gauss-seidel spectral radius is 0.9873554 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 14:11:17 rms-change max change #iterations 0.1571508 21.09790 at 10iterations 1.5809307E-02 1.992306 at 20iterations 1.6996022E-03 0.2392159 at 30iterations 2.4635930E-04 3.5503387E-02 at 40iterations 4.9836352E-05 7.5893402E-03 at 50iterations finished qdiffx linear iterations at : 14:11:20 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 4.9836352E-05 7.5893402E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 14:11:20 3.202u 0.144s 0:03.67 91.0% 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 Sat Oct 8 2011 at 14:11:20 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.918551 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): -11.33300 44.33400 ymin,ymax (A): 10.69000 54.73700 zmin,zma (A): 41.43200 94.31700 x,y,z range (A): 55.66700 44.04700 52.88500 scale (grids/A): 1.918551 object centre (A): 16.50050 32.71350 67.87450 number of atom coordinates read : 2925 total number of charged atoms : 2781 net assigned charge : -0.9859930 assigned positive charge : 438.0637 centred at (gu) : 86.65363 88.70888 90.63611 assigned negative charge : -439.0505 centred at (gu) : 86.57463 88.49138 90.54311 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23342 grid for indexing accessible points = 1.400000 m= 32579 mr = 63400 m= 5044 mr = 24753 m= 249 mr = 3091 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 34003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21892 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) : 0.6395171 object centre at (A) : 16.50050 32.71350 67.87450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3269207E-02 5.1663457E-03 midg,1,midg; midg,igrid,midg -3.8284997E-03 1.3881942E-02 1,midg,midg; igrid,midg,midg -1.8713932E-02 1.6010642E-02 gauss-seidel spectral radius is 0.9986800 estimated iterations to convergence 218 setup time was (sec) 0.8800000 now iterating at: 14:11:21 rms-change max change #iterations 4.642012 223.6451 at 10iterations 2.215577 78.41685 at 20iterations 1.051663 32.80319 at 30iterations 0.4983182 14.33801 at 40iterations 0.2365905 7.099590 at 50iterations 0.1127546 3.096275 at 60iterations 5.3617317E-02 1.534663 at 70iterations 2.5470698E-02 0.7566986 at 80iterations 1.2102257E-02 0.3570099 at 90iterations 5.7878448E-03 0.1702957 at 100iterations 2.7561113E-03 7.6587677E-02 at 110iterations 1.3172106E-03 3.7584305E-02 at 120iterations finished qdiffx linear iterations at : 14:11:27 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 1.3172106E-03 3.7584305E-02 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 14:11:28 7.233u 0.183s 0:07.72 95.9% 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 14:11:28 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.877827 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): -11.33300 44.33400 ymin,ymax (A): 10.69000 54.73700 zmin,zma (A): 41.43200 94.31700 x,y,z range (A): 55.66700 44.04700 52.88500 scale (grids/A): 2.877827 object centre (A): 16.50050 32.71350 67.87450 number of atom coordinates read : 2925 total number of charged atoms : 2781 net assigned charge : -0.9859930 assigned positive charge : 438.0637 centred at (gu) : 84.98026 88.06314 90.95400 assigned negative charge : -439.0505 centred at (gu) : 84.86181 87.73695 90.81459 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 202315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23342 grid for indexing accessible points = 1.400000 m= 105868 mr = 153058 m= 38517 mr = 88514 m= 9119 mr = 31303 m= 1197 mr = 6676 m= 46 mr = 798 m= 0 mr = 4 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 76709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 22248 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) : 1.918551 object centre at (A) : 16.50050 32.71350 67.87450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6361256E-03 0.1132240 midg,1,midg; midg,igrid,midg -1.2316956E-02 0.1322425 1,midg,midg; igrid,midg,midg -9.7771786E-02 0.4118076 gauss-seidel spectral radius is 0.9992722 estimated iterations to convergence 293 setup time was (sec) 1.870000 now iterating at: 14:11:30 rms-change max change #iterations 10.83505 398.0912 at 10iterations 6.401206 141.1257 at 20iterations 3.757150 74.67389 at 30iterations 2.199474 50.35915 at 40iterations 1.282049 24.62350 at 50iterations 0.7476236 12.50690 at 60iterations 0.4339942 9.022241 at 70iterations 0.2522806 4.630993 at 80iterations 0.1461336 2.738400 at 90iterations 8.4780253E-02 1.426080 at 100iterations 4.9177874E-02 0.9188905 at 110iterations 2.8465789E-02 0.5753696 at 120iterations 1.6492182E-02 0.2690125 at 130iterations 9.5668929E-03 0.1557312 at 140iterations 5.5729882E-03 9.3198776E-02 at 150iterations 3.2542944E-03 5.3316116E-02 at 160iterations 1.9138202E-03 3.1337738E-02 at 170iterations 1.1391065E-03 1.7826080E-02 at 180iterations finished qdiffx linear iterations at : 14:11:40 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 1.1391065E-03 1.7826080E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 14:11:40 11.649u 0.182s 0:12.17 97.1% 0+0k 0+0io 0pf+0w