Sun Oct 9 08:10:36 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 08:10:36 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3440 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5065741 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): -28.94500 41.33100 ymin,ymax (A): -5.793000 48.29900 zmin,zma (A): -15.91400 38.99900 x,y,z range (A): 70.27600 54.09200 54.91300 scale (grids/A): 0.5065741 object centre (A): 6.192999 21.25300 11.54250 number of atom coordinates read : 3440 total number of charged atoms : 3300 net assigned charge : 11.00003 assigned positive charge : 512.6685 centred at (gu) : 88.07780 88.76446 89.43948 assigned negative charge : -501.6698 centred at (gu) : 88.03195 88.81896 89.45525 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5809 nv = 96 ne = 84 npr = 66757 no. pairs analyzed = 66757 no. exposed pairs = 4585 no. arc points = 33566 no. surface atoms = 1531 nbur = 1909 mkacc time = 0.1400000 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 = 1.708000 m= 192 mr = 2768 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3303 ## 528 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7741 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7765908E-10 9.1523407E-11 midg,1,midg; midg,igrid,midg 2.9371877E-10 3.4445266E-11 1,midg,midg; igrid,midg,midg 9.5373008E-11 1.2090674E-10 gauss-seidel spectral radius is 0.9799921 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 08:10:37 rms-change max change #iterations 5.2919894E-02 10.43722 at 10iterations 2.8999576E-03 0.5421667 at 20iterations 1.8716935E-04 3.0014038E-02 at 30iterations 1.9455838E-05 2.6121140E-03 at 40iterations 2.7734079E-06 3.9672852E-04 at 50iterations finished qdiffx linear iterations at : 08:10:39 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 2.7734079E-06 3.9672852E-04 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 08:10:40 3.148u 0.144s 0:03.56 92.1% 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 Sun Oct 9 2011 at 08:10:40 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3440 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.519722 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): -28.94500 41.33100 ymin,ymax (A): -5.793000 48.29900 zmin,zma (A): -15.91400 38.99900 x,y,z range (A): 70.27600 54.09200 54.91300 scale (grids/A): 1.519722 object centre (A): 6.192999 21.25300 11.54250 number of atom coordinates read : 3440 total number of charged atoms : 3300 net assigned charge : 11.00003 assigned positive charge : 512.6685 centred at (gu) : 84.23263 86.29234 88.31770 assigned negative charge : -501.6698 centred at (gu) : 84.09547 86.45655 88.36493 start vw surface at 0.1900000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 64997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33566 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 17278 mr = 42108 m= 1418 mr = 10914 m= 22 mr = 593 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 30100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 495 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 24712 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) : 0.5065741 object centre at (A) : 6.192999 21.25300 11.54250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7841945E-03 2.4767038E-03 midg,1,midg; midg,igrid,midg 9.7831506E-03 1.5659065E-03 1,midg,midg; igrid,midg,midg -1.4726946E-03 3.0901791E-03 gauss-seidel spectral radius is 0.9979513 estimated iterations to convergence 176 setup time was (sec) 0.7400000 now iterating at: 08:10:41 rms-change max change #iterations 3.010138 141.3717 at 10iterations 1.186492 50.28622 at 20iterations 0.4656682 18.28831 at 30iterations 0.1832146 7.086781 at 40iterations 7.2186597E-02 2.833035 at 50iterations 2.8553803E-02 1.041721 at 60iterations 1.1256002E-02 0.4422712 at 70iterations 4.4287620E-03 0.1611810 at 80iterations 1.7539604E-03 6.9503546E-02 at 90iterations 6.9338863E-04 2.4932861E-02 at 100iterations 2.7445695E-04 1.0051966E-02 at 110iterations 1.0846974E-04 3.8394928E-03 at 120iterations finished qdiffx linear iterations at : 08:10:47 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 1.0846974E-04 3.8394928E-03 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 08:10:47 6.874u 0.161s 0:07.35 95.6% 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 08:10:47 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3440 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: 2.279583 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): -28.94500 41.33100 ymin,ymax (A): -5.793000 48.29900 zmin,zma (A): -15.91400 38.99900 x,y,z range (A): 70.27600 54.09200 54.91300 scale (grids/A): 2.279583 object centre (A): 6.192999 21.25300 11.54250 number of atom coordinates read : 3440 total number of charged atoms : 3300 net assigned charge : 11.00003 assigned positive charge : 512.6685 centred at (gu) : 81.34880 84.43833 87.47638 assigned negative charge : -501.6698 centred at (gu) : 81.14321 84.68458 87.54734 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 151532 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33566 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 62496 mr = 104030 m= 14905 mr = 47231 m= 2010 mr = 10461 m= 78 mr = 1218 m= 0 mr = 10 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 68071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 26319 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) : 1.519722 object centre at (A) : 6.192999 21.25300 11.54250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1483065 1.4218077E-02 midg,1,midg; midg,igrid,midg 0.1477944 2.0541819E-03 1,midg,midg; igrid,midg,midg -0.1464132 6.9645472E-02 gauss-seidel spectral radius is 0.9990790 estimated iterations to convergence 260 setup time was (sec) 1.310000 now iterating at: 08:10:49 rms-change max change #iterations 8.291661 270.8863 at 10iterations 4.660393 123.2702 at 20iterations 2.574787 66.65078 at 30iterations 1.417085 37.78646 at 40iterations 0.7752532 18.39835 at 50iterations 0.4218674 10.13504 at 60iterations 0.2289149 5.601692 at 70iterations 0.1242232 2.682343 at 80iterations 6.7129120E-02 1.414951 at 90iterations 3.6345217E-02 1.101964 at 100iterations 1.9601524E-02 0.4024067 at 110iterations 1.0583012E-02 0.2214384 at 120iterations 5.6977598E-03 0.1198769 at 130iterations 3.0763736E-03 6.3755035E-02 at 140iterations 1.6570236E-03 3.6377221E-02 at 150iterations 8.9262147E-04 1.7519474E-02 at 160iterations 4.8084973E-04 9.5386505E-03 at 170iterations 2.5926123E-04 5.0668716E-03 at 180iterations finished qdiffx linear iterations at : 08:10:58 total time elapsed so far: 10.76000 # loops : 180 mean,max change (kT/e) : 2.5926123E-04 5.0668716E-03 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.92000 DelPhi exited at 08:10:59 10.927u 0.168s 0:11.53 96.0% 0+0k 0+0io 0pf+0w