Sun Oct 9 07:21:09 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 Sun Oct 9 2011 at 07:21:09 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2521 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5439433 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): -3.880000 42.10300 ymin,ymax (A): 35.75400 87.52700 zmin,zma (A): -3.856000 61.59200 x,y,z range (A): 45.98300 51.77300 65.44800 scale (grids/A): 0.5439433 object centre (A): 19.11150 61.64050 28.86800 number of atom coordinates read : 2521 total number of charged atoms : 2375 net assigned charge : -10.49998 assigned positive charge : 377.2549 centred at (gu) : 90.50635 89.16330 89.74870 assigned negative charge : -387.7553 centred at (gu) : 90.66570 88.79931 89.66074 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4911 nv = 96 ne = 84 npr = 50063 no. pairs analyzed = 50063 no. exposed pairs = 3491 no. arc points = 25127 no. surface atoms = 1177 nbur = 1344 mkacc time = 7.9999998E-02 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 = 1.568000 m= 196 mr = 2336 m= 0 mr = 2 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2424 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1175871E-09 -1.0241304E-10 midg,1,midg; midg,igrid,midg -3.2311571E-09 1.0415546E-09 1,midg,midg; igrid,midg,midg 2.2892974E-10 -1.6392806E-09 gauss-seidel spectral radius is 0.9825482 estimated iterations to convergence 62 setup time was (sec) 0.3700000 now iterating at: 07:21:10 rms-change max change #iterations 6.4560570E-02 13.83211 at 10iterations 4.3121143E-03 0.7557411 at 20iterations 2.7102057E-04 5.0341606E-02 at 30iterations 1.7722474E-05 3.1185150E-03 at 40iterations 1.2051680E-06 2.0837784E-04 at 50iterations finished qdiffx linear iterations at : 07:21:12 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.2051680E-06 2.0837784E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 07:21:13 3.337u 0.166s 0:03.99 87.4% 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 Sun Oct 9 2011 at 07:21:13 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2521 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.631830 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): -3.880000 42.10300 ymin,ymax (A): 35.75400 87.52700 zmin,zma (A): -3.856000 61.59200 x,y,z range (A): 45.98300 51.77300 65.44800 scale (grids/A): 1.631830 object centre (A): 19.11150 61.64050 28.86800 number of atom coordinates read : 2521 total number of charged atoms : 2375 net assigned charge : -10.49998 assigned positive charge : 377.2549 centred at (gu) : 91.51850 87.48920 89.24537 assigned negative charge : -387.7553 centred at (gu) : 91.99673 86.39776 88.98195 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 54027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25127 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15837 mr = 34348 m= 1413 mr = 10447 m= 28 mr = 588 m= 0 mr = 2 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 25920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 18196 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) : 0.5439433 object centre at (A) : 19.11150 61.64050 28.86800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4029868E-02 3.9471867E-03 midg,1,midg; midg,igrid,midg -2.2503320E-02 7.1354392E-03 1,midg,midg; igrid,midg,midg -2.9694238E-03 -1.5130442E-02 gauss-seidel spectral radius is 0.9981338 estimated iterations to convergence 184 setup time was (sec) 0.4800000 now iterating at: 07:21:14 rms-change max change #iterations 3.004871 147.2002 at 10iterations 1.239176 62.25957 at 20iterations 0.5070955 20.33488 at 30iterations 0.2082423 8.196992 at 40iterations 8.5416295E-02 3.433856 at 50iterations 3.5095543E-02 1.372541 at 60iterations 1.4407851E-02 0.6465712 at 70iterations 5.9222193E-03 0.2384844 at 80iterations 2.4415627E-03 9.7042084E-02 at 90iterations 1.0028088E-03 3.7731171E-02 at 100iterations 4.1211632E-04 1.7060280E-02 at 110iterations 1.6970873E-04 7.0724487E-03 at 120iterations finished qdiffx linear iterations at : 07:21:21 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 1.6970873E-04 7.0724487E-03 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 07:21:21 7.503u 0.196s 0:07.97 96.4% 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 Sun Oct 9 2011 at 07:21:21 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2521 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.447745 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): -3.880000 42.10300 ymin,ymax (A): 35.75400 87.52700 zmin,zma (A): -3.856000 61.59200 x,y,z range (A): 45.98300 51.77300 65.44800 scale (grids/A): 2.447745 object centre (A): 19.11150 61.64050 28.86800 number of atom coordinates read : 2521 total number of charged atoms : 2375 net assigned charge : -10.49998 assigned positive charge : 377.2549 centred at (gu) : 92.27764 86.23370 88.86805 assigned negative charge : -387.7553 centred at (gu) : 92.99505 84.59658 88.47283 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 125095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25127 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 55670 mr = 84234 m= 14465 mr = 43062 m= 2040 mr = 10423 m= 128 mr = 1219 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 58434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18976 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) : 1.631830 object centre at (A) : 19.11150 61.64050 28.86800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8603255 5.6201436E-02 midg,1,midg; midg,igrid,midg -0.3030286 9.8176420E-02 1,midg,midg; igrid,midg,midg -4.4434913E-02 -0.1945270 gauss-seidel spectral radius is 0.9991120 estimated iterations to convergence 265 setup time was (sec) 0.8800000 now iterating at: 07:21:22 rms-change max change #iterations 7.927398 299.5195 at 10iterations 4.370010 135.9673 at 20iterations 2.415148 65.19510 at 30iterations 1.328048 31.51999 at 40iterations 0.7294469 20.06794 at 50iterations 0.4007686 10.38941 at 60iterations 0.2188737 5.006925 at 70iterations 0.1195000 2.804635 at 80iterations 6.5222740E-02 1.470524 at 90iterations 3.5644729E-02 0.7325776 at 100iterations 1.9430898E-02 0.4408379 at 110iterations 1.0559089E-02 0.2414083 at 120iterations 5.7504717E-03 0.1301308 at 130iterations 3.1258573E-03 6.9316983E-02 at 140iterations 1.6995337E-03 4.1393280E-02 at 150iterations 9.2776690E-04 2.0639420E-02 at 160iterations 5.0465181E-04 1.1325836E-02 at 170iterations 2.7365546E-04 6.4635277E-03 at 180iterations finished qdiffx linear iterations at : 07:21:33 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 2.7365546E-04 6.4635277E-03 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 07:21:33 11.872u 0.189s 0:12.34 97.6% 0+0k 0+0io 0pf+0w