Tue Oct 11 06:20:29 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 06:20:29 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 = 2064 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.6952582 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): -15.31400 24.98000 ymin,ymax (A): -0.7409999 40.64800 zmin,zma (A): 0.7459999 51.95000 x,y,z range (A): 40.29400 41.38900 51.20400 scale (grids/A): 0.6952582 object centre (A): 4.833000 19.95350 26.34800 number of atom coordinates read : 2064 total number of charged atoms : 1933 net assigned charge : 6.025006 assigned positive charge : 314.8841 centred at (gu) : 90.71919 89.25007 90.27711 assigned negative charge : -308.8591 centred at (gu) : 90.84637 89.13604 90.28967 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6810 nv = 96 ne = 84 npr = 41463 no. pairs analyzed = 41463 no. exposed pairs = 2429 no. arc points = 16923 no. surface atoms = 830 nbur = 1234 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3903 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1709 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7668 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1110333E-08 3.5884874E-08 midg,1,midg; midg,igrid,midg -5.1422520E-09 6.9487662E-08 1,midg,midg; igrid,midg,midg 7.4023603E-08 -1.0881764E-08 gauss-seidel spectral radius is 0.9892178 estimated iterations to convergence 78 setup time was (sec) 0.6800000 now iterating at: 06:20:30 rms-change max change #iterations 0.1886881 25.83824 at 10iterations 2.2783009E-02 3.409459 at 20iterations 3.0161915E-03 0.5129414 at 30iterations 5.3078588E-04 6.8647385E-02 at 40iterations 1.3651501E-04 1.5625000E-02 at 50iterations finished qdiffx linear iterations at : 06:20:34 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 1.3651501E-04 1.5625000E-02 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 06:20:34 4.681u 0.442s 0:05.63 90.9% 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 06:20:35 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 = 2064 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.085775 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): -15.31400 24.98000 ymin,ymax (A): -0.7409999 40.64800 zmin,zma (A): 0.7459999 51.95000 x,y,z range (A): 40.29400 41.38900 51.20400 scale (grids/A): 2.085775 object centre (A): 4.833000 19.95350 26.34800 number of atom coordinates read : 2064 total number of charged atoms : 1933 net assigned charge : 6.025006 assigned positive charge : 314.8841 centred at (gu) : 92.15742 87.75021 90.83131 assigned negative charge : -308.8591 centred at (gu) : 92.53934 87.40819 90.86927 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72143 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16923 grid for indexing accessible points = 1.400000 m= 28377 mr = 51342 m= 5271 mr = 21622 m= 475 mr = 3431 m= 12 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 29632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15358 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) : 0.6952582 object centre at (A) : 4.833000 19.95350 26.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4685025E-02 4.6100944E-02 midg,1,midg; midg,igrid,midg 3.3381989E-03 2.0043183E-02 1,midg,midg; igrid,midg,midg 3.4604881E-02 -9.4869756E-05 gauss-seidel spectral radius is 0.9987928 estimated iterations to convergence 228 setup time was (sec) 1.080000 now iterating at: 06:20:36 rms-change max change #iterations 4.475739 206.7893 at 10iterations 2.192098 76.19223 at 20iterations 1.073229 34.23183 at 30iterations 0.5279583 16.24697 at 40iterations 0.2588533 8.617537 at 50iterations 0.1266373 3.733222 at 60iterations 6.2571608E-02 2.024696 at 70iterations 3.0738285E-02 0.9813328 at 80iterations 1.5139983E-02 0.4658165 at 90iterations 7.5178742E-03 0.2790222 at 100iterations 3.7425580E-03 0.1148987 at 110iterations 1.8843905E-03 5.7697296E-02 at 120iterations finished qdiffx linear iterations at : 06:20:46 total time elapsed so far: 10.76000 # loops : 120 mean,max change (kT/e) : 1.8843905E-03 5.7697296E-02 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.97000 DelPhi exited at 06:20:46 10.978u 0.494s 0:11.79 97.2% 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 06:20:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.128662 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): -15.31400 24.98000 ymin,ymax (A): -0.7409999 40.64800 zmin,zma (A): 0.7459999 51.95000 x,y,z range (A): 40.29400 41.38900 51.20400 scale (grids/A): 3.128662 object centre (A): 4.833000 19.95350 26.34800 number of atom coordinates read : 2064 total number of charged atoms : 1933 net assigned charge : 6.025006 assigned positive charge : 314.8841 centred at (gu) : 93.23621 86.62548 91.24708 assigned negative charge : -308.8591 centred at (gu) : 93.80905 86.11228 91.30390 start vw surface at 0.1400000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 166320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16923 grid for indexing accessible points = 1.400000 m= 89785 mr = 123677 m= 35357 mr = 74819 m= 9792 mr = 28998 m= 1931 mr = 7564 m= 223 mr = 1396 m= 7 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.340000 number of dielectric boundary points 66813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 15464 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) : 2.085775 object centre at (A) : 4.833000 19.95350 26.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3407530 0.3004309 midg,1,midg; midg,igrid,midg 6.0570117E-02 0.1458026 1,midg,midg; igrid,midg,midg 0.3354073 9.2413677E-03 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 2.730000 now iterating at: 06:20:50 rms-change max change #iterations 10.06025 396.4926 at 10iterations 5.903081 126.9548 at 20iterations 3.472187 70.25586 at 30iterations 2.029330 40.55809 at 40iterations 1.187770 25.12007 at 50iterations 0.6944256 16.19583 at 60iterations 0.4047979 7.323574 at 70iterations 0.2359439 4.155127 at 80iterations 0.1377755 2.417319 at 90iterations 8.0413640E-02 1.548964 at 100iterations 4.6985574E-02 0.7834377 at 110iterations 2.7548850E-02 0.5146618 at 120iterations 1.6245227E-02 0.2942142 at 130iterations 9.7461119E-03 0.1748838 at 140iterations 5.9706625E-03 0.1104279 at 150iterations 3.7918242E-03 7.7268600E-02 at 160iterations 2.5241333E-03 4.7405243E-02 at 170iterations 1.7843109E-03 3.5144806E-02 at 180iterations finished qdiffx linear iterations at : 06:21:06 total time elapsed so far: 18.93000 # loops : 180 mean,max change (kT/e) : 1.7843109E-03 3.5144806E-02 energy calculations done at 18.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.16000 DelPhi exited at 06:21:07 19.160u 0.514s 0:20.42 96.3% 0+0k 0+0io 0pf+0w