Tue Oct 11 03:45:10 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 Tue Oct 11 2011 at 03:45:10 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: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6513347 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): -7.086000 44.47600 ymin,ymax (A): 27.36600 82.02299 zmin,zma (A): -27.99300 24.39800 x,y,z range (A): 51.56200 54.65700 52.39100 scale (grids/A): 0.6513347 object centre (A): 18.69500 54.69450 -1.797501 number of atom coordinates read : 2787 total number of charged atoms : 2666 net assigned charge : 2.588017 assigned positive charge : 431.4066 centred at (gu) : 89.41870 89.01897 90.95486 assigned negative charge : -428.8191 centred at (gu) : 89.39631 88.90920 90.66733 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7988 nv = 96 ne = 84 npr = 54493 no. pairs analyzed = 54493 no. exposed pairs = 3603 no. arc points = 25289 no. surface atoms = 1213 nbur = 1574 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4361 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2000000 number of dielectric boundary points 4029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2380 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9497 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8039509E-08 6.5756204E-08 midg,1,midg; midg,igrid,midg -1.7867359E-08 1.9411436E-08 1,midg,midg; igrid,midg,midg 1.1574656E-09 7.8563707E-09 gauss-seidel spectral radius is 0.9878044 estimated iterations to convergence 74 setup time was (sec) 0.3900000 now iterating at: 03:45:10 rms-change max change #iterations 0.1685698 24.53052 at 10iterations 1.7564110E-02 2.274326 at 20iterations 1.9017393E-03 0.3174038 at 30iterations 2.3253115E-04 3.2735825E-02 at 40iterations 3.9055889E-05 6.1702728E-03 at 50iterations finished qdiffx linear iterations at : 03:45:13 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 3.9055889E-05 6.1702728E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 03:45:14 3.363u 0.167s 0:04.06 86.6% 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 Tue Oct 11 2011 at 03:45:14 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: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.954004 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): -7.086000 44.47600 ymin,ymax (A): 27.36600 82.02299 zmin,zma (A): -27.99300 24.39800 x,y,z range (A): 51.56200 54.65700 52.39100 scale (grids/A): 1.954004 object centre (A): 18.69500 54.69450 -1.797501 number of atom coordinates read : 2787 total number of charged atoms : 2666 net assigned charge : 2.588017 assigned positive charge : 431.4066 centred at (gu) : 88.25562 87.05619 92.86423 assigned negative charge : -428.8191 centred at (gu) : 88.18880 86.72702 92.00174 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25289 grid for indexing accessible points = 1.400000 m= 32278 mr = 57601 m= 5590 mr = 23872 m= 366 mr = 3529 m= 5 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1097 time to turn everything in is 0.4200000 number of dielectric boundary points 37328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 21039 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) : 0.6513347 object centre at (A) : 18.69500 54.69450 -1.797501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4863271E-03 0.1258183 midg,1,midg; midg,igrid,midg -5.2724201E-02 1.7454959E-02 1,midg,midg; igrid,midg,midg -3.8995095E-02 -2.4888765E-02 gauss-seidel spectral radius is 0.9987288 estimated iterations to convergence 222 setup time was (sec) 0.6300000 now iterating at: 03:45:15 rms-change max change #iterations 4.778219 211.9101 at 10iterations 2.309474 74.80684 at 20iterations 1.113098 35.11035 at 30iterations 0.5360799 17.48845 at 40iterations 0.2577616 8.050247 at 50iterations 0.1243266 3.814654 at 60iterations 5.9755839E-02 1.772381 at 70iterations 2.8772915E-02 0.8268623 at 80iterations 1.3887377E-02 0.4087753 at 90iterations 6.6903085E-03 0.1843481 at 100iterations 3.2236448E-03 9.6735477E-02 at 110iterations 1.5612817E-03 4.5692444E-02 at 120iterations finished qdiffx linear iterations at : 03:45:22 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.5612817E-03 4.5692444E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 03:45:22 7.790u 0.190s 0:08.33 95.7% 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 Tue Oct 11 2011 at 03:45:22 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: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.931006 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): -7.086000 44.47600 ymin,ymax (A): 27.36600 82.02299 zmin,zma (A): -27.99300 24.39800 x,y,z range (A): 51.56200 54.65700 52.39100 scale (grids/A): 2.931006 object centre (A): 18.69500 54.69450 -1.797501 number of atom coordinates read : 2787 total number of charged atoms : 2666 net assigned charge : 2.588017 assigned positive charge : 431.4066 centred at (gu) : 87.38338 85.58421 94.29601 assigned negative charge : -428.8191 centred at (gu) : 87.28323 85.09054 93.00250 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 194355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25289 grid for indexing accessible points = 1.400000 m= 101365 mr = 139679 m= 39436 mr = 82608 m= 10162 mr = 31940 m= 1512 mr = 7581 m= 93 mr = 983 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 3844 time to turn everything in is 1.100000 number of dielectric boundary points 84109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 21320 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) : 1.954004 object centre at (A) : 18.69500 54.69450 -1.797501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9393767E-02 1.382509 midg,1,midg; midg,igrid,midg -0.5562134 -8.1000790E-02 1,midg,midg; igrid,midg,midg -0.5743921 -0.3868576 gauss-seidel spectral radius is 0.9992988 estimated iterations to convergence 298 setup time was (sec) 1.330000 now iterating at: 03:45:24 rms-change max change #iterations 11.18259 501.7310 at 10iterations 6.666771 138.9093 at 20iterations 3.958480 93.74499 at 30iterations 2.343421 45.69505 at 40iterations 1.382674 26.52001 at 50iterations 0.8162529 14.71646 at 60iterations 0.4794182 9.476425 at 70iterations 0.2819822 5.230038 at 80iterations 0.1651506 2.949537 at 90iterations 9.6806228E-02 1.828557 at 100iterations 5.6758337E-02 1.041813 at 110iterations 3.3225719E-02 0.5616096 at 120iterations 1.9477921E-02 0.3218384 at 130iterations 1.1390968E-02 0.1943073 at 140iterations 6.6839438E-03 0.1146822 at 150iterations 3.9095110E-03 6.4699173E-02 at 160iterations 2.2969723E-03 3.8715363E-02 at 170iterations 1.3584237E-03 2.3296356E-02 at 180iterations finished qdiffx linear iterations at : 03:45:35 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 1.3584237E-03 2.3296356E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 03:45:36 12.870u 0.214s 0:13.59 96.2% 0+0k 0+0io 0pf+0w