Wed Feb 15 08:58:12 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:58:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: NAP 500 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: 0.6520266 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 0.6520266 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9999929 assigned positive charge : 449.1386 centred at (gu) : 88.94199 89.58736 91.91899 assigned negative charge : -450.1394 centred at (gu) : 88.95462 89.47089 91.84512 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8328 nv = 96 ne = 84 npr = 64578 no. pairs analyzed = 64578 no. exposed pairs = 3410 no. arc points = 23500 no. surface atoms = 1169 nbur = 1827 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 4883 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.4400000 number of dielectric boundary points 3841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2274 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0720226E-08 1.7321589E-08 midg,1,midg; midg,igrid,midg -2.6369660E-08 1.7495244E-08 1,midg,midg; igrid,midg,midg 1.6167012E-10 -3.6795862E-09 gauss-seidel spectral radius is 0.9878368 estimated iterations to convergence 74 setup time was (sec) 0.7200000 now iterating at: 08:58:13 rms-change max change #iterations 0.1756084 23.80111 at 10iterations 1.8677993E-02 2.419418 at 20iterations 2.0112211E-03 0.2782888 at 30iterations 2.4749062E-04 3.4065247E-02 at 40iterations 4.1257324E-05 5.4016113E-03 at 50iterations finished qdiffx linear iterations at : 08:58:17 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 4.1257324E-05 5.4016113E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 08:58:17 4.495u 0.422s 0:05.31 92.4% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:58:18 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 = 2996 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.956080 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 1.956080 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9999929 assigned positive charge : 449.1386 centred at (gu) : 86.82532 88.76170 95.75655 assigned negative charge : -450.1394 centred at (gu) : 86.86359 88.41257 95.53489 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 90618 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23500 grid for indexing accessible points = 1.400000 m= 33728 mr = 65450 m= 5380 mr = 25445 m= 392 mr = 3504 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 791 time to turn everything in is 0.8900000 number of dielectric boundary points 35588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 22468 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) : 0.6520266 object centre at (A) : 15.13650 -0.1445007 19.46450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1974249E-02 2.3345828E-02 midg,1,midg; midg,igrid,midg -1.7068856E-03 2.1974105E-02 1,midg,midg; igrid,midg,midg -4.2748842E-02 1.4454820E-03 gauss-seidel spectral radius is 0.9987294 estimated iterations to convergence 222 setup time was (sec) 1.220000 now iterating at: 08:58:19 rms-change max change #iterations 4.865827 200.7043 at 10iterations 2.352041 74.61267 at 20iterations 1.132545 32.62309 at 30iterations 0.5465869 16.37157 at 40iterations 0.2629251 7.561531 at 50iterations 0.1264543 3.510738 at 60iterations 6.0966816E-02 1.914815 at 70iterations 2.9403724E-02 0.9240646 at 80iterations 1.4194060E-02 0.4324493 at 90iterations 6.8510822E-03 0.1938992 at 100iterations 3.3109591E-03 0.1107998 at 110iterations 1.6020127E-03 4.3675423E-02 at 120iterations finished qdiffx linear iterations at : 08:58:29 total time elapsed so far: 10.89000 # loops : 120 mean,max change (kT/e) : 1.6020127E-03 4.3675423E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 08:58:30 11.101u 0.471s 0:11.89 97.3% 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 Wed Feb 15 2012 at 08:58:30 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 = 2996 !!! WARNING: NAP 500 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.934120 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 2.934120 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9999929 assigned positive charge : 449.1386 centred at (gu) : 85.23785 88.14234 98.63457 assigned negative charge : -450.1394 centred at (gu) : 85.29537 87.61875 98.30231 start vw surface at 0.1600000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 209619 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23500 grid for indexing accessible points = 1.400000 m= 109040 mr = 157771 m= 39897 mr = 90846 m= 9887 mr = 32642 m= 1541 mr = 7555 m= 105 mr = 1073 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 1.460000 no. cavity mid-points inaccessible to solvent = 2722 time to turn everything in is 2.410000 number of dielectric boundary points 80160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.580000 number of grid points assigned charge 22791 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) : 1.956080 object centre at (A) : 15.13650 -0.1445007 19.46450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0269648E-02 0.3441303 midg,1,midg; midg,igrid,midg -6.3514193E-03 0.2455389 1,midg,midg; igrid,midg,midg -0.6238739 0.2748454 gauss-seidel spectral radius is 0.9992867 estimated iterations to convergence 295 setup time was (sec) 2.800000 now iterating at: 08:58:33 rms-change max change #iterations 11.24041 368.4833 at 10iterations 6.608460 136.3396 at 20iterations 3.881162 80.87073 at 30iterations 2.270804 42.68746 at 40iterations 1.326920 23.55063 at 50iterations 0.7743185 14.36628 at 60iterations 0.4500960 7.229960 at 70iterations 0.2624403 4.786066 at 80iterations 0.1527300 2.482361 at 90iterations 8.8956736E-02 1.359652 at 100iterations 5.1728658E-02 0.8234386 at 110iterations 3.0050229E-02 0.4811964 at 120iterations 1.7495293E-02 0.2927017 at 130iterations 1.0157029E-02 0.1693420 at 140iterations 5.9211897E-03 0.1003594 at 150iterations 3.4541318E-03 5.9368134E-02 at 160iterations 2.0248289E-03 3.3790588E-02 at 170iterations 1.1870259E-03 2.0059586E-02 at 180iterations finished qdiffx linear iterations at : 08:58:52 total time elapsed so far: 22.11000 # loops : 180 mean,max change (kT/e) : 1.1870259E-03 2.0059586E-02 energy calculations done at 22.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.35000 DelPhi exited at 08:58:53 22.350u 0.448s 0:23.09 98.7% 0+0k 0+0io 0pf+0w