Sun Oct 9 19:29:04 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 19:29:04 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5431 !!! WARNING: ASL 282 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5183384 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): 3.116000 67.24800 ymin,ymax (A): -9.302999 55.84900 zmin,zma (A): -1.947000 66.73400 x,y,z range (A): 64.13200 65.15200 68.68100 scale (grids/A): 0.5183384 object centre (A): 35.18200 23.27300 32.39350 number of atom coordinates read : 5431 total number of charged atoms : 5253 net assigned charge : 4.654041 assigned positive charge : 837.0830 centred at (gu) : 88.28815 88.75851 88.64242 assigned negative charge : -832.4351 centred at (gu) : 88.16119 88.77734 88.56942 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9027 nv = 96 ne = 84 npr = 112462 no. pairs analyzed = 112462 no. exposed pairs = 6069 no. arc points = 41549 no. surface atoms = 2080 nbur = 3351 mkacc time = 0.1900000 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 = 1.652000 m= 327 mr = 5068 m= 1 mr = 6 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 0.3600000 number of dielectric boundary points 4281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4189 ## 588 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12337 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8892902E-10 2.8577973E-10 midg,1,midg; midg,igrid,midg 2.5422847E-10 2.1058207E-11 1,midg,midg; igrid,midg,midg -6.8170658E-10 4.0050466E-10 gauss-seidel spectral radius is 0.9809957 estimated iterations to convergence 60 setup time was (sec) 0.5500000 now iterating at: 19:29:04 rms-change max change #iterations 8.5423611E-02 11.88498 at 10iterations 9.9101262E-03 1.500763 at 20iterations 3.5415252E-03 0.6214447 at 30iterations 1.4733619E-03 0.2560577 at 40iterations 6.2108517E-04 0.1055145 at 50iterations finished qdiffx linear iterations at : 19:29:07 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 6.2108517E-04 0.1055145 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 19:29:08 3.593u 0.189s 0:04.06 92.8% 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 19:29:08 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5431 !!! WARNING: ASL 282 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.555015 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): 3.116000 67.24800 ymin,ymax (A): -9.302999 55.84900 zmin,zma (A): -1.947000 66.73400 x,y,z range (A): 64.13200 65.15200 68.68100 scale (grids/A): 1.555015 object centre (A): 35.18200 23.27300 32.39350 number of atom coordinates read : 5431 total number of charged atoms : 5253 net assigned charge : 4.654041 assigned positive charge : 837.0830 centred at (gu) : 84.86283 86.27412 85.92552 assigned negative charge : -832.4351 centred at (gu) : 84.48333 86.33177 85.70798 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 31188 mr = 75754 m= 2850 mr = 21678 m= 78 mr = 1221 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 39860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 542 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 39613 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) : 0.5183384 object centre at (A) : 35.18200 23.27300 32.39350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4419200E-02 1.3136881E-02 midg,1,midg; midg,igrid,midg 1.9731982E-02 1.7501522E-02 1,midg,midg; igrid,midg,midg -1.3107653E-02 8.4527722E-03 gauss-seidel spectral radius is 0.9982073 estimated iterations to convergence 188 setup time was (sec) 0.7400000 now iterating at: 19:29:09 rms-change max change #iterations 4.332048 159.9713 at 10iterations 1.820114 64.50943 at 20iterations 0.7635852 22.12014 at 30iterations 0.3219230 9.634739 at 40iterations 0.1360360 4.205158 at 50iterations 5.8512077E-02 1.996513 at 60iterations 2.6045252E-02 0.8073387 at 70iterations 1.2719986E-02 0.3781433 at 80iterations 7.1732863E-03 0.2405853 at 90iterations 4.5916145E-03 0.1650352 at 100iterations 3.2080610E-03 0.1080093 at 110iterations 2.3200796E-03 7.7270508E-02 at 120iterations finished qdiffx linear iterations at : 19:29:16 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 2.3200796E-03 7.7270508E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 19:29:16 8.104u 0.185s 0:08.55 96.8% 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 19:29:16 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5431 !!! WARNING: ASL 282 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.332523 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): 3.116000 67.24800 ymin,ymax (A): -9.302999 55.84900 zmin,zma (A): -1.947000 66.73400 x,y,z range (A): 64.13200 65.15200 68.68100 scale (grids/A): 2.332523 object centre (A): 35.18200 23.27300 32.39350 number of atom coordinates read : 5431 total number of charged atoms : 5253 net assigned charge : 4.654041 assigned positive charge : 837.0830 centred at (gu) : 82.29369 84.41100 83.88808 assigned negative charge : -832.4351 centred at (gu) : 81.72506 84.49749 83.56174 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 244150 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 111885 mr = 185445 m= 29140 mr = 89868 m= 4170 mr = 21543 m= 221 mr = 2550 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 90085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 41921 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) : 1.555015 object centre at (A) : 35.18200 23.27300 32.39350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4949039 0.6019236 midg,1,midg; midg,igrid,midg 0.3519031 0.3482080 1,midg,midg; igrid,midg,midg -0.3057005 8.3217196E-02 gauss-seidel spectral radius is 0.9991871 estimated iterations to convergence 277 setup time was (sec) 1.480000 now iterating at: 19:29:18 rms-change max change #iterations 11.34022 327.9763 at 10iterations 6.514204 139.7087 at 20iterations 3.708194 70.31567 at 30iterations 2.102733 43.38415 at 40iterations 1.186726 26.35278 at 50iterations 0.6700960 11.98650 at 60iterations 0.3774928 6.632317 at 70iterations 0.2125914 4.496593 at 80iterations 0.1198458 2.173398 at 90iterations 6.7682497E-02 1.242188 at 100iterations 3.8534753E-02 0.8109379 at 110iterations 2.2203501E-02 0.4850836 at 120iterations 1.3168224E-02 0.2329559 at 130iterations 8.1760874E-03 0.1630898 at 140iterations 5.3888294E-03 0.1173515 at 150iterations 3.8172719E-03 8.3580017E-02 at 160iterations 2.8754608E-03 5.9814453E-02 at 170iterations 2.2504132E-03 4.5127869E-02 at 180iterations finished qdiffx linear iterations at : 19:29:30 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 2.2504132E-03 4.5127869E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 19:29:30 13.375u 0.219s 0:13.87 97.9% 0+0k 0+0io 0pf+0w