Mon Oct 10 14:00:02 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+sph.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 = amb.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 Mon Oct 10 2011 at 14:00:02 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7187853 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): 20.50500 66.99400 ymin,ymax (A): -24.25400 25.27400 zmin,zma (A): -4.401000 34.87600 x,y,z range (A): 46.48900 49.52800 39.27700 scale (grids/A): 0.7187853 object centre (A): 43.74950 0.5100002 15.23750 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 90.01140 90.61233 90.62859 assigned negative charge : -327.3089 centred at (gu) : 89.91611 90.70551 90.76325 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7660 nv = 96 ne = 84 npr = 45958 no. pairs analyzed = 45958 no. exposed pairs = 2779 no. arc points = 19585 no. surface atoms = 932 nbur = 1288 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 4217 m= 7 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.3600000 number of dielectric boundary points 3838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1734 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8502 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3785943E-07 -2.7391845E-08 midg,1,midg; midg,igrid,midg 1.1436558E-07 4.5573501E-09 1,midg,midg; igrid,midg,midg 3.1070340E-09 1.3013748E-07 gauss-seidel spectral radius is 0.9899255 estimated iterations to convergence 81 setup time was (sec) 0.5800000 now iterating at: 14:00:03 rms-change max change #iterations 0.2220862 29.94575 at 10iterations 2.8193733E-02 3.722904 at 20iterations 3.5363063E-03 0.4741049 at 30iterations 4.5489476E-04 5.5076599E-02 at 40iterations 5.8461803E-05 7.9808235E-03 at 50iterations finished qdiffx linear iterations at : 14:00:05 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.8461803E-05 7.9808235E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:00:07 3.413u 0.159s 0:04.64 76.7% 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 Mon Oct 10 2011 at 14:00:07 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 2.156356 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): 20.50500 66.99400 ymin,ymax (A): -24.25400 25.27400 zmin,zma (A): -4.401000 34.87600 x,y,z range (A): 46.48900 49.52800 39.27700 scale (grids/A): 2.156356 object centre (A): 43.74950 0.5100002 15.23750 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 90.03395 91.83668 91.88546 assigned negative charge : -327.3089 centred at (gu) : 89.74822 92.11655 92.28979 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 80945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19585 grid for indexing accessible points = 1.400000 m= 31114 mr = 55703 m= 6467 mr = 23484 m= 686 mr = 4403 m= 35 mr = 381 m= 0 mr = 9 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1107 time to turn everything in is 0.6600000 number of dielectric boundary points 35267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 16569 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) : 0.7187853 object centre at (A) : 43.74950 0.5100002 15.23750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7311695E-02 5.5715661E-03 midg,1,midg; midg,igrid,midg 4.0864624E-02 3.3314671E-02 1,midg,midg; igrid,midg,midg -1.4500574E-02 4.6595030E-02 gauss-seidel spectral radius is 0.9988782 estimated iterations to convergence 236 setup time was (sec) 0.9200000 now iterating at: 14:00:08 rms-change max change #iterations 4.902607 177.3351 at 10iterations 2.468362 86.20325 at 20iterations 1.237709 40.59588 at 30iterations 0.6213440 18.84006 at 40iterations 0.3121236 9.478588 at 50iterations 0.1561665 4.342884 at 60iterations 7.8692839E-02 2.317030 at 70iterations 3.9634798E-02 1.115074 at 80iterations 1.9932754E-02 0.6501617 at 90iterations 9.9822562E-03 0.3101425 at 100iterations 5.0191716E-03 0.1406937 at 110iterations 2.5223147E-03 6.8441391E-02 at 120iterations finished qdiffx linear iterations at : 14:00:14 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 2.5223147E-03 6.8441391E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 14:00:15 7.153u 0.228s 0:07.98 92.3% 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 Mon Oct 10 2011 at 14:00:15 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.234534 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): 20.50500 66.99400 ymin,ymax (A): -24.25400 25.27400 zmin,zma (A): -4.401000 34.87600 x,y,z range (A): 46.48900 49.52800 39.27700 scale (grids/A): 3.234534 object centre (A): 43.74950 0.5100002 15.23750 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 90.05079 92.75489 92.82816 assigned negative charge : -327.3089 centred at (gu) : 89.62223 93.17496 93.43475 start vw surface at 0.1500000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 186626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19585 grid for indexing accessible points = 1.400000 m= 96611 mr = 134612 m= 39938 mr = 79491 m= 12277 mr = 33123 m= 2648 mr = 9597 m= 425 mr = 1956 m= 59 mr = 316 m= 0 mr = 44 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 3596 time to turn everything in is 1.900000 number of dielectric boundary points 79445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 16664 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) : 2.156356 object centre at (A) : 43.74950 0.5100002 15.23750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7071325 9.7041978E-03 midg,1,midg; midg,igrid,midg 0.2846618 0.4794225 1,midg,midg; igrid,midg,midg -7.4473538E-02 0.3370742 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.190000 now iterating at: 14:00:17 rms-change max change #iterations 10.70749 352.0159 at 10iterations 6.237878 132.3685 at 20iterations 3.635359 65.68417 at 30iterations 2.122694 37.67950 at 40iterations 1.240156 21.52706 at 50iterations 0.7237709 13.17256 at 60iterations 0.4213879 6.755690 at 70iterations 0.2455395 4.125896 at 80iterations 0.1430245 2.368042 at 90iterations 8.3332650E-02 1.398478 at 100iterations 4.8604589E-02 0.8319428 at 110iterations 2.8290695E-02 0.5192890 at 120iterations 1.6495999E-02 0.2716089 at 130iterations 9.6054161E-03 0.1568356 at 140iterations 5.6155208E-03 9.4879150E-02 at 150iterations 3.2725416E-03 5.0407410E-02 at 160iterations 1.9050246E-03 3.2016754E-02 at 170iterations 1.1123577E-03 1.8852234E-02 at 180iterations finished qdiffx linear iterations at : 14:00:27 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 1.1123577E-03 1.8852234E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 14:00:29 12.686u 0.178s 0:14.23 90.3% 0+0k 0+0io 0pf+0w