Sun Oct 9 13:17:46 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 Sun Oct 9 2011 at 13:17:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 0.6925800 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): -4.903000 43.93300 ymin,ymax (A): -14.35400 37.04800 zmin,zma (A): 2.235000 44.98100 x,y,z range (A): 48.83600 51.40200 42.74600 scale (grids/A): 0.6925800 object centre (A): 19.51500 11.34700 23.60800 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500020 assigned positive charge : 362.6770 centred at (gu) : 89.16219 91.03439 90.53024 assigned negative charge : -360.1775 centred at (gu) : 89.17243 91.23464 90.58080 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7690 nv = 96 ne = 84 npr = 48549 no. pairs analyzed = 48549 no. exposed pairs = 3013 no. arc points = 21139 no. surface atoms = 1001 nbur = 1384 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 4233 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2016 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8780 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2634514E-08 -5.4476499E-09 midg,1,midg; midg,igrid,midg 7.7628499E-08 -8.3239080E-08 1,midg,midg; igrid,midg,midg 2.3551502E-08 9.9712043E-09 gauss-seidel spectral radius is 0.9891683 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 13:17:47 rms-change max change #iterations 0.1931265 29.35418 at 10iterations 2.3626195E-02 3.125275 at 20iterations 3.1270452E-03 0.3842621 at 30iterations 5.7628093E-04 8.4474564E-02 at 40iterations 1.6089226E-04 2.4810791E-02 at 50iterations finished qdiffx linear iterations at : 13:17:50 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.6089226E-04 2.4810791E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 13:17:50 3.333u 0.173s 0:03.84 91.1% 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 13:17:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 2.077740 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): -4.903000 43.93300 ymin,ymax (A): -14.35400 37.04800 zmin,zma (A): 2.235000 44.98100 x,y,z range (A): 48.83600 51.40200 42.74600 scale (grids/A): 2.077740 object centre (A): 19.51500 11.34700 23.60800 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500020 assigned positive charge : 362.6770 centred at (gu) : 87.48608 93.10247 91.59019 assigned negative charge : -360.1775 centred at (gu) : 87.51696 93.70367 91.74194 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21139 grid for indexing accessible points = 1.400000 m= 31143 mr = 57045 m= 5409 mr = 23061 m= 495 mr = 3439 m= 10 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 35340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17807 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) : 0.6925800 object centre at (A) : 19.51500 11.34700 23.60800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3135293E-02 1.2745652E-02 midg,1,midg; midg,igrid,midg 2.2840573E-02 -7.3143326E-02 1,midg,midg; igrid,midg,midg 5.3739369E-02 -1.2082484E-02 gauss-seidel spectral radius is 0.9988241 estimated iterations to convergence 231 setup time was (sec) 0.6500000 now iterating at: 13:17:51 rms-change max change #iterations 4.859415 184.7047 at 10iterations 2.393460 88.11369 at 20iterations 1.181417 34.63314 at 30iterations 0.5855511 18.53491 at 40iterations 0.2886742 8.841962 at 50iterations 0.1433177 4.385024 at 60iterations 7.1096644E-02 2.203308 at 70iterations 3.5402920E-02 1.039940 at 80iterations 1.7581025E-02 0.5408688 at 90iterations 8.8128326E-03 0.2767715 at 100iterations 4.5073605E-03 0.1321192 at 110iterations 2.3617873E-03 6.8710566E-02 at 120iterations finished qdiffx linear iterations at : 13:17:58 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 2.3617873E-03 6.8710566E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 13:17:59 8.018u 0.181s 0:08.47 96.6% 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 13:17:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 3.116610 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): -4.903000 43.93300 ymin,ymax (A): -14.35400 37.04800 zmin,zma (A): 2.235000 44.98100 x,y,z range (A): 48.83600 51.40200 42.74600 scale (grids/A): 3.116610 object centre (A): 19.51500 11.34700 23.60800 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500020 assigned positive charge : 362.6770 centred at (gu) : 86.22899 94.65367 92.38506 assigned negative charge : -360.1775 centred at (gu) : 86.27533 95.55542 92.61299 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 189149 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21139 grid for indexing accessible points = 1.400000 m= 98663 mr = 137709 m= 37873 mr = 80999 m= 10168 mr = 30596 m= 1972 mr = 7657 m= 227 mr = 1367 m= 9 mr = 160 m= 0 mr = 1 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 79572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 17942 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) : 2.077740 object centre at (A) : 19.51500 11.34700 23.60800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4420190 2.4725465E-02 midg,1,midg; midg,igrid,midg 0.5068010 -0.8155113 1,midg,midg; igrid,midg,midg 0.6966912 -0.3377388 gauss-seidel spectral radius is 0.9992976 estimated iterations to convergence 298 setup time was (sec) 1.450000 now iterating at: 13:18:00 rms-change max change #iterations 10.88185 429.3376 at 10iterations 6.427894 134.5395 at 20iterations 3.793206 68.59628 at 30iterations 2.239647 39.87093 at 40iterations 1.318514 27.37579 at 50iterations 0.7753867 14.45140 at 60iterations 0.4550539 8.979660 at 70iterations 0.2664768 4.725223 at 80iterations 0.1562344 2.625233 at 90iterations 9.1677792E-02 1.593117 at 100iterations 5.3895671E-02 0.9689293 at 110iterations 3.1684048E-02 0.5162824 at 120iterations 1.8769175E-02 0.3326836 at 130iterations 1.1288593E-02 0.2588997 at 140iterations 6.9509908E-03 0.1348248 at 150iterations 4.4571673E-03 8.7814331E-02 at 160iterations 3.0232340E-03 6.2168121E-02 at 170iterations 2.1856446E-03 4.5604706E-02 at 180iterations finished qdiffx linear iterations at : 13:18:12 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 2.1856446E-03 4.5604706E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 13:18:12 12.939u 0.228s 0:13.45 97.7% 0+0k 0+0io 0pf+0w