Sat Oct 8 13:00:02 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 13:00:02 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1303 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6956929 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): -1.003000 39.60100 ymin,ymax (A): -19.56500 22.96400 zmin,zma (A): -16.99600 34.17600 x,y,z range (A): 40.60400 42.52900 51.17200 scale (grids/A): 0.6956929 object centre (A): 19.29900 1.699499 8.590001 number of atom coordinates read : 1303 total number of charged atoms : 1168 net assigned charge : 3.000018 assigned positive charge : 193.7503 centred at (gu) : 90.24486 88.87681 90.41936 assigned negative charge : -190.7500 centred at (gu) : 90.33341 88.70313 89.86785 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4226 nv = 96 ne = 84 npr = 26080 no. pairs analyzed = 26080 no. exposed pairs = 1760 no. arc points = 12682 no. surface atoms = 586 nbur = 717 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 245 mr = 2106 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 2336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1030 ## 78 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4561 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0597647E-07 1.5248717E-07 midg,1,midg; midg,igrid,midg -2.7264086E-08 4.7219370E-08 1,midg,midg; igrid,midg,midg 3.7898570E-08 -1.3113555E-09 gauss-seidel spectral radius is 0.9891648 estimated iterations to convergence 78 setup time was (sec) 0.3200000 now iterating at: 13:00:03 rms-change max change #iterations 0.1486024 29.69525 at 10iterations 1.7025530E-02 3.586771 at 20iterations 1.9871085E-03 0.3219066 at 30iterations 2.3767780E-04 3.9661407E-02 at 40iterations 2.8200633E-05 4.4937134E-03 at 50iterations finished qdiffx linear iterations at : 13:00:06 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 2.8200633E-05 4.4937134E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 13:00:06 3.627u 0.233s 0:04.14 92.9% 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 13:00:06 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1303 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.087079 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): -1.003000 39.60100 ymin,ymax (A): -19.56500 22.96400 zmin,zma (A): -16.99600 34.17600 x,y,z range (A): 40.60400 42.52900 51.17200 scale (grids/A): 2.087079 object centre (A): 19.29900 1.699499 8.590001 number of atom coordinates read : 1303 total number of charged atoms : 1168 net assigned charge : 3.000018 assigned positive charge : 193.7503 centred at (gu) : 90.73487 86.63067 91.25838 assigned negative charge : -190.7500 centred at (gu) : 91.00024 86.10928 89.60355 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 44266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12682 grid for indexing accessible points = 1.400000 m= 15573 mr = 28398 m= 2705 mr = 11024 m= 215 mr = 1686 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 21560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9253 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) : 0.6956929 object centre at (A) : 19.29900 1.699499 8.590001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7766230E-02 9.1758274E-02 midg,1,midg; midg,igrid,midg -2.2739090E-02 2.1542842E-02 1,midg,midg; igrid,midg,midg 6.1627291E-04 -3.3534602E-03 gauss-seidel spectral radius is 0.9987208 estimated iterations to convergence 221 setup time was (sec) 0.4900000 now iterating at: 13:00:07 rms-change max change #iterations 3.497315 184.0036 at 10iterations 1.656206 70.14452 at 20iterations 0.7939605 35.10892 at 30iterations 0.3765505 15.45148 at 40iterations 0.1810075 7.533542 at 50iterations 8.6334862E-02 3.227779 at 60iterations 4.1290849E-02 1.600578 at 70iterations 1.9760408E-02 0.7333708 at 80iterations 9.4652297E-03 0.3811989 at 90iterations 4.5319893E-03 0.1917763 at 100iterations 2.1658195E-03 8.8272095E-02 at 110iterations 1.0312562E-03 3.8896769E-02 at 120iterations finished qdiffx linear iterations at : 13:00:15 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 1.0312562E-03 3.8896769E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 13:00:15 8.383u 0.249s 0:08.93 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 Sat Oct 8 2011 at 13:00:15 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1303 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.130618 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): -1.003000 39.60100 ymin,ymax (A): -19.56500 22.96400 zmin,zma (A): -16.99600 34.17600 x,y,z range (A): 40.60400 42.52900 51.17200 scale (grids/A): 3.130618 object centre (A): 19.29900 1.699499 8.590001 number of atom coordinates read : 1303 total number of charged atoms : 1168 net assigned charge : 3.000018 assigned positive charge : 193.7503 centred at (gu) : 91.10239 84.94594 91.88765 assigned negative charge : -190.7500 centred at (gu) : 91.50036 84.16392 89.40532 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 102083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12682 grid for indexing accessible points = 1.400000 m= 48917 mr = 69118 m= 18345 mr = 38843 m= 4872 mr = 14468 m= 943 mr = 3617 m= 114 mr = 678 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 48501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 9344 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) : 2.087079 object centre at (A) : 19.29900 1.699499 8.590001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0189909E-02 0.9363508 midg,1,midg; midg,igrid,midg -0.2391475 0.2062597 1,midg,midg; igrid,midg,midg 2.7931981E-02 -1.3988432E-03 gauss-seidel spectral radius is 0.9992621 estimated iterations to convergence 291 setup time was (sec) 0.9900000 now iterating at: 13:00:17 rms-change max change #iterations 7.888627 401.9755 at 10iterations 4.502988 115.2074 at 20iterations 2.580048 66.16856 at 30iterations 1.479159 35.42006 at 40iterations 0.8478699 20.37610 at 50iterations 0.4862536 10.86002 at 60iterations 0.2780352 5.779233 at 70iterations 0.1590449 3.609187 at 80iterations 9.1278322E-02 2.105264 at 90iterations 5.2140344E-02 1.280167 at 100iterations 2.9907718E-02 0.6100006 at 110iterations 1.7159501E-02 0.3779979 at 120iterations 9.8353596E-03 0.2232080 at 130iterations 5.6236046E-03 0.1230412 at 140iterations 3.2247724E-03 7.9025269E-02 at 150iterations 1.8427412E-03 4.1795731E-02 at 160iterations 1.0609329E-03 2.3893356E-02 at 170iterations 6.0598139E-04 1.3957977E-02 at 180iterations finished qdiffx linear iterations at : 13:00:29 total time elapsed so far: 13.54000 # loops : 180 mean,max change (kT/e) : 6.0598139E-04 1.3957977E-02 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.67000 DelPhi exited at 13:00:30 13.676u 0.256s 0:14.21 97.9% 0+0k 0+0io 0pf+0w