Sat Oct 8 12:19:07 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 12:19:07 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 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: 0.5078749 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): -60.00900 10.08700 ymin,ymax (A): -38.29800 18.16400 zmin,zma (A): -4.442000 54.53600 x,y,z range (A): 70.09600 56.46200 58.97800 scale (grids/A): 0.5078749 object centre (A): -24.96100 -10.06700 25.04700 number of atom coordinates read : 2959 total number of charged atoms : 2820 net assigned charge : -0.9999670 assigned positive charge : 406.6914 centred at (gu) : 93.27214 89.52206 89.63857 assigned negative charge : -407.6924 centred at (gu) : 93.11586 89.45878 89.62273 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5191 nv = 96 ne = 84 npr = 59804 no. pairs analyzed = 59804 no. exposed pairs = 4372 no. arc points = 31176 no. surface atoms = 1472 nbur = 1487 mkacc time = 0.1600000 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 = 1.680000 m= 155 mr = 2114 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3026 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 6669 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3720100E-11 1.2334862E-12 midg,1,midg; midg,igrid,midg -1.1594420E-10 5.4820006E-11 1,midg,midg; igrid,midg,midg -9.5662624E-11 4.4174056E-10 gauss-seidel spectral radius is 0.9800683 estimated iterations to convergence 59 setup time was (sec) 0.6400000 now iterating at: 12:19:08 rms-change max change #iterations 4.6438716E-02 8.550125 at 10iterations 4.2794035E-03 0.9620094 at 20iterations 1.2906287E-03 0.3436394 at 30iterations 4.7131293E-04 0.1254578 at 40iterations 1.7230357E-04 4.5932770E-02 at 50iterations finished qdiffx linear iterations at : 12:19:11 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.7230357E-04 4.5932770E-02 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 12:19:12 4.228u 0.295s 0:04.83 93.3% 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 12:19:12 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 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: 1.523625 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): -60.00900 10.08700 ymin,ymax (A): -38.29800 18.16400 zmin,zma (A): -4.442000 54.53600 x,y,z range (A): 70.09600 56.46200 58.97800 scale (grids/A): 1.523625 object centre (A): -24.96100 -10.06700 25.04700 number of atom coordinates read : 2959 total number of charged atoms : 2820 net assigned charge : -0.9999670 assigned positive charge : 406.6914 centred at (gu) : 99.81567 88.56541 88.91480 assigned negative charge : -407.6924 centred at (gu) : 99.34741 88.37601 88.86768 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 56695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31176 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 14534 mr = 33969 m= 1273 mr = 8298 m= 27 mr = 382 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 29880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 21282 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) : 0.5078749 object centre at (A) : -24.96100 -10.06700 25.04700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8516197E-03 5.7343603E-03 midg,1,midg; midg,igrid,midg -2.8001929E-03 3.3658044E-03 1,midg,midg; igrid,midg,midg -2.9349357E-03 5.1239640E-03 gauss-seidel spectral radius is 0.9979231 estimated iterations to convergence 175 setup time was (sec) 0.8600000 now iterating at: 12:19:13 rms-change max change #iterations 2.674849 144.0477 at 10iterations 1.037828 46.33488 at 20iterations 0.4065444 17.73840 at 30iterations 0.1590599 6.572075 at 40iterations 6.2082704E-02 2.475561 at 50iterations 2.4736989E-02 0.9820061 at 60iterations 1.0199497E-02 0.4374199 at 70iterations 4.6306932E-03 0.2447815 at 80iterations 2.4147274E-03 0.1260529 at 90iterations 1.4757790E-03 7.8353882E-02 at 100iterations 9.8191807E-04 5.1628113E-02 at 110iterations 6.7492540E-04 3.5476685E-02 at 120iterations finished qdiffx linear iterations at : 12:19:21 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 6.7492540E-04 3.5476685E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 12:19:22 9.450u 0.315s 0:10.05 97.1% 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 12:19:22 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 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: 2.285437 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): -60.00900 10.08700 ymin,ymax (A): -38.29800 18.16400 zmin,zma (A): -4.442000 54.53600 x,y,z range (A): 70.09600 56.46200 58.97800 scale (grids/A): 2.285437 object centre (A): -24.96100 -10.06700 25.04700 number of atom coordinates read : 2959 total number of charged atoms : 2820 net assigned charge : -0.9999670 assigned positive charge : 406.6914 centred at (gu) : 104.7233 87.84794 88.37213 assigned negative charge : -407.6924 centred at (gu) : 104.0211 87.56396 88.30145 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 131758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31176 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 52123 mr = 85488 m= 12903 mr = 36521 m= 1610 mr = 8212 m= 60 mr = 787 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 67435 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 22493 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) : 1.523625 object centre at (A) : -24.96100 -10.06700 25.04700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0405580E-02 0.1013500 midg,1,midg; midg,igrid,midg -4.3661706E-02 6.3544989E-02 1,midg,midg; igrid,midg,midg -3.5665616E-02 0.1419520 gauss-seidel spectral radius is 0.9990572 estimated iterations to convergence 257 setup time was (sec) 1.610000 now iterating at: 12:19:24 rms-change max change #iterations 7.411257 230.8065 at 10iterations 4.102387 121.0607 at 20iterations 2.257756 66.22813 at 30iterations 1.236600 32.11783 at 40iterations 0.6735845 18.11814 at 50iterations 0.3658123 10.11619 at 60iterations 0.1982228 5.093877 at 70iterations 0.1067773 2.658217 at 80iterations 5.7421118E-02 1.348858 at 90iterations 3.0862218E-02 0.7060318 at 100iterations 1.6684929E-02 0.3895452 at 110iterations 8.9735081E-03 0.2080288 at 120iterations 4.8468006E-03 0.1099396 at 130iterations 2.6319663E-03 6.0948014E-02 at 140iterations 1.4526243E-03 3.7258148E-02 at 150iterations 8.3034969E-04 2.2052765E-02 at 160iterations 4.9751782E-04 1.5174866E-02 at 170iterations 3.2109313E-04 8.9950562E-03 at 180iterations finished qdiffx linear iterations at : 12:19:38 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 3.2109313E-04 8.9950562E-03 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 12:19:38 15.592u 0.340s 0:16.22 98.2% 0+0k 0+0io 0pf+0w