Mon Oct 10 17:04:58 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 Mon Oct 10 2011 at 17:04:58 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 !!! WARNING: HIT 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6564995 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): 24.58000 76.88200 ymin,ymax (A): 7.645000 53.55500 zmin,zma (A): -11.60600 42.62100 x,y,z range (A): 52.30200 45.91000 54.22700 scale (grids/A): 0.6564995 object centre (A): 50.73100 30.60000 15.50750 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : -6.985985 assigned positive charge : 288.1610 centred at (gu) : 90.01361 89.11308 87.98312 assigned negative charge : -295.1469 centred at (gu) : 90.29066 89.32140 88.35285 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5741 nv = 96 ne = 84 npr = 40409 no. pairs analyzed = 40409 no. exposed pairs = 2703 no. arc points = 19754 no. surface atoms = 907 nbur = 1061 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 277 mr = 2762 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2600000 number of dielectric boundary points 3235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1884 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9140560E-08 -4.5989811E-08 midg,1,midg; midg,igrid,midg 1.3059503E-08 -3.8647361E-08 1,midg,midg; igrid,midg,midg 1.9519401E-08 -5.6574653E-08 gauss-seidel spectral radius is 0.9879292 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 17:04:59 rms-change max change #iterations 0.1508361 27.13180 at 10iterations 1.5784262E-02 2.455247 at 20iterations 1.5922351E-03 0.2550411 at 30iterations 1.6528866E-04 2.5497437E-02 at 40iterations 1.7312042E-05 2.6626587E-03 at 50iterations finished qdiffx linear iterations at : 17:05:01 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.7312042E-05 2.6626587E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 17:05:02 3.343u 0.183s 0:04.29 82.0% 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 Mon Oct 10 2011 at 17:05:02 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 !!! WARNING: HIT 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.969499 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): 24.58000 76.88200 ymin,ymax (A): 7.645000 53.55500 zmin,zma (A): -11.60600 42.62100 x,y,z range (A): 52.30200 45.91000 54.22700 scale (grids/A): 1.969499 object centre (A): 50.73100 30.60000 15.50750 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : -6.985985 assigned positive charge : 288.1610 centred at (gu) : 90.04094 87.33926 83.94941 assigned negative charge : -295.1469 centred at (gu) : 90.87194 87.96413 85.05827 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 61672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19754 grid for indexing accessible points = 1.400000 m= 19292 mr = 39438 m= 2648 mr = 13143 m= 154 mr = 1413 m= 6 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 575 time to turn everything in is 0.4900000 number of dielectric boundary points 29715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14516 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) : 0.6564995 object centre at (A) : 50.73100 30.60000 15.50750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3409482E-02 -4.2399716E-02 midg,1,midg; midg,igrid,midg 2.8169559E-02 -1.8065102E-02 1,midg,midg; igrid,midg,midg -2.3160456E-02 -5.1488291E-02 gauss-seidel spectral radius is 0.9986644 estimated iterations to convergence 217 setup time was (sec) 0.7900000 now iterating at: 17:05:03 rms-change max change #iterations 3.924363 181.4180 at 10iterations 1.842952 94.17505 at 20iterations 0.8615137 28.71365 at 30iterations 0.4061185 13.60642 at 40iterations 0.1908686 6.543709 at 50iterations 9.0094708E-02 3.279945 at 60iterations 4.2381160E-02 1.534149 at 70iterations 1.9888781E-02 0.6964874 at 80iterations 9.4210682E-03 0.3296051 at 90iterations 4.4218311E-03 0.1551876 at 100iterations 2.0799770E-03 7.4417114E-02 at 110iterations 9.7889069E-04 3.2639503E-02 at 120iterations finished qdiffx linear iterations at : 17:05:11 total time elapsed so far: 8.640000 # loops : 120 mean,max change (kT/e) : 9.7889069E-04 3.2639503E-02 energy calculations done at 8.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.830000 DelPhi exited at 17:05:12 8.831u 0.209s 0:09.35 96.5% 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 Mon Oct 10 2011 at 17:05:12 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 !!! WARNING: HIT 148 has a net charge of 0.5140 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: 2.954248 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): 24.58000 76.88200 ymin,ymax (A): 7.645000 53.55500 zmin,zma (A): -11.60600 42.62100 x,y,z range (A): 52.30200 45.91000 54.22700 scale (grids/A): 2.954248 object centre (A): 50.73100 30.60000 15.50750 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : -6.985985 assigned positive charge : 288.1610 centred at (gu) : 90.06139 86.00882 80.92413 assigned negative charge : -295.1469 centred at (gu) : 91.30785 86.94613 82.58739 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 142496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19754 grid for indexing accessible points = 1.400000 m= 64195 mr = 96235 m= 20927 mr = 50059 m= 4463 mr = 15862 m= 643 mr = 3051 m= 42 mr = 415 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1996 time to turn everything in is 1.190000 number of dielectric boundary points 67123 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14688 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) : 1.969499 object centre at (A) : 50.73100 30.60000 15.50750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5888257 -0.3571226 midg,1,midg; midg,igrid,midg 0.2712758 -0.1709704 1,midg,midg; igrid,midg,midg -0.3532051 -0.5042917 gauss-seidel spectral radius is 0.9992697 estimated iterations to convergence 292 setup time was (sec) 1.510000 now iterating at: 17:05:13 rms-change max change #iterations 9.126149 382.4014 at 10iterations 5.328707 130.9364 at 20iterations 3.103600 72.91269 at 30iterations 1.793844 40.32053 at 40iterations 1.038161 24.16479 at 50iterations 0.5971282 13.83059 at 60iterations 0.3455912 6.527725 at 70iterations 0.1987406 3.742785 at 80iterations 0.1142916 2.405272 at 90iterations 6.5774381E-02 1.391563 at 100iterations 3.7807766E-02 0.7422714 at 110iterations 2.1728683E-02 0.4166260 at 120iterations 1.2513569E-02 0.2336721 at 130iterations 7.1943202E-03 0.1420059 at 140iterations 4.1460893E-03 8.6956024E-02 at 150iterations 2.3773061E-03 4.6527684E-02 at 160iterations 1.3704767E-03 2.5215149E-02 at 170iterations 7.8875385E-04 1.5790939E-02 at 180iterations finished qdiffx linear iterations at : 17:05:24 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 7.8875385E-04 1.5790939E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 17:05:25 12.554u 0.218s 0:13.43 95.0% 0+0k 0+0io 0pf+0w