Mon Oct 10 14:00:00 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 Mon Oct 10 2011 at 14:00:00 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 !!! WARNING: SEP 61 has a net charge of -0.4750 !!! WARNING: GLM 117 has a net charge of -0.0940 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: 0.5994174 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): -2.207000 57.18400 ymin,ymax (A): -23.58300 29.19700 zmin,zma (A): -9.685000 44.84200 x,y,z range (A): 59.39100 52.78000 54.52700 scale (grids/A): 0.5994174 object centre (A): 27.48850 2.807000 17.57850 number of atom coordinates read : 3374 total number of charged atoms : 3221 net assigned charge : 4.931024 assigned positive charge : 506.4527 centred at (gu) : 91.95477 88.65089 90.18196 assigned negative charge : -501.5231 centred at (gu) : 91.96785 88.63267 90.20570 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 70266 no. pairs analyzed = 70266 no. exposed pairs = 3833 no. arc points = 26822 no. surface atoms = 1303 nbur = 2071 mkacc time = 0.2000000 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 = 1.456000 m= 339 mr = 4472 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4400000 number of dielectric boundary points 3741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2735 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0497089E-09 1.0306132E-09 midg,1,midg; midg,igrid,midg 1.6634826E-09 2.1693314E-09 1,midg,midg; igrid,midg,midg 1.7491012E-09 2.2716649E-09 gauss-seidel spectral radius is 0.9856532 estimated iterations to convergence 68 setup time was (sec) 0.7100000 now iterating at: 14:00:01 rms-change max change #iterations 0.1253718 16.68163 at 10iterations 1.0875048E-02 1.436402 at 20iterations 9.8800834E-04 0.1510496 at 30iterations 1.0914826E-04 1.5998840E-02 at 40iterations 1.9369008E-05 2.3031235E-03 at 50iterations finished qdiffx linear iterations at : 14:00:04 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.9369008E-05 2.3031235E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 14:00:06 4.211u 0.260s 0:06.06 73.7% 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 14:00:06 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 !!! WARNING: SEP 61 has a net charge of -0.4750 !!! WARNING: GLM 117 has a net charge of -0.0940 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: 1.798252 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): -2.207000 57.18400 ymin,ymax (A): -23.58300 29.19700 zmin,zma (A): -9.685000 44.84200 x,y,z range (A): 59.39100 52.78000 54.52700 scale (grids/A): 1.798252 object centre (A): 27.48850 2.807000 17.57850 number of atom coordinates read : 3374 total number of charged atoms : 3221 net assigned charge : 4.931024 assigned positive charge : 506.4527 centred at (gu) : 95.86353 85.95171 90.54485 assigned negative charge : -501.5231 centred at (gu) : 95.90300 85.89778 90.61674 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 87012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26822 grid for indexing accessible points = 1.400000 m= 29782 mr = 62298 m= 3787 mr = 21758 m= 155 mr = 2141 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1646 time to turn everything in is 0.7700000 number of dielectric boundary points 34492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 25146 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) : 0.5994174 object centre at (A) : 27.48850 2.807000 17.57850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0966238E-03 -2.0327948E-02 midg,1,midg; midg,igrid,midg 6.6053616E-03 1.1116629E-02 1,midg,midg; igrid,midg,midg 2.7391534E-02 3.0082598E-02 gauss-seidel spectral radius is 0.9985400 estimated iterations to convergence 208 setup time was (sec) 1.080000 now iterating at: 14:00:07 rms-change max change #iterations 4.365184 171.1800 at 10iterations 1.994201 73.23226 at 20iterations 0.9088542 33.03827 at 30iterations 0.4161278 13.71724 at 40iterations 0.1897209 5.809761 at 50iterations 8.6757138E-02 2.697776 at 60iterations 3.9626759E-02 1.138916 at 70iterations 1.8156929E-02 0.5528717 at 80iterations 8.3105359E-03 0.2636738 at 90iterations 3.7992890E-03 0.1268387 at 100iterations 1.7401119E-03 5.3012371E-02 at 110iterations 7.9675537E-04 2.4149895E-02 at 120iterations finished qdiffx linear iterations at : 14:00:16 total time elapsed so far: 9.530000 # loops : 120 mean,max change (kT/e) : 7.9675537E-04 2.4149895E-02 energy calculations done at 9.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 14:00:17 9.711u 0.282s 0:11.02 90.6% 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 Mon Oct 10 2011 at 14:00:17 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 !!! WARNING: SEP 61 has a net charge of -0.4750 !!! WARNING: GLM 117 has a net charge of -0.0940 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: 2.697378 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): -2.207000 57.18400 ymin,ymax (A): -23.58300 29.19700 zmin,zma (A): -9.685000 44.84200 x,y,z range (A): 59.39100 52.78000 54.52700 scale (grids/A): 2.697378 object centre (A): 27.48850 2.807000 17.57850 number of atom coordinates read : 3374 total number of charged atoms : 3221 net assigned charge : 4.931024 assigned positive charge : 506.4527 centred at (gu) : 98.79503 83.92737 90.81709 assigned negative charge : -501.5231 centred at (gu) : 98.85452 83.84655 90.92516 start vw surface at 0.1800000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 202136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26822 grid for indexing accessible points = 1.400000 m= 99963 mr = 151335 m= 32275 mr = 81922 m= 6202 mr = 25348 m= 597 mr = 4447 m= 30 mr = 362 m= 0 mr = 2 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 5354 time to turn everything in is 1.920000 number of dielectric boundary points 77787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 25763 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) : 1.798252 object centre at (A) : 27.48850 2.807000 17.57850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2621274E-02 -0.2355005 midg,1,midg; midg,igrid,midg 1.4737265E-03 0.1109209 1,midg,midg; igrid,midg,midg 0.3039955 0.3638341 gauss-seidel spectral radius is 0.9992464 estimated iterations to convergence 288 setup time was (sec) 2.250000 now iterating at: 14:00:20 rms-change max change #iterations 10.55062 285.4450 at 10iterations 6.162568 116.5236 at 20iterations 3.566578 76.86045 at 30iterations 2.063754 40.91438 at 40iterations 1.187736 22.37621 at 50iterations 0.6829486 13.40124 at 60iterations 0.3926759 7.608392 at 70iterations 0.2253018 4.473857 at 80iterations 0.1293889 2.345764 at 90iterations 7.4126214E-02 1.394943 at 100iterations 4.2423140E-02 0.7535105 at 110iterations 2.4279024E-02 0.4272795 at 120iterations 1.3930688E-02 0.2358093 at 130iterations 7.9925517E-03 0.1381478 at 140iterations 4.5940224E-03 8.4290028E-02 at 150iterations 2.6407568E-03 4.7508240E-02 at 160iterations 1.5203177E-03 2.5455475E-02 at 170iterations 8.8043645E-04 1.6101837E-02 at 180iterations finished qdiffx linear iterations at : 14:00:34 total time elapsed so far: 16.36000 # loops : 180 mean,max change (kT/e) : 8.8043645E-04 1.6101837E-02 energy calculations done at 16.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.54000 DelPhi exited at 14:00:35 16.543u 0.322s 0:17.44 96.6% 0+0k 0+0io 0pf+0w