Mon Oct 10 18:51:50 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 18:51:50 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: SEP 33 has a net charge of -0.4750 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: MG6 661 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5775002 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): 45.59600 104.0240 ymin,ymax (A): 8.777000 70.42200 zmin,zma (A): 19.98400 63.63400 x,y,z range (A): 58.42800 61.64500 43.65000 scale (grids/A): 0.5775002 object centre (A): 74.81000 39.59950 41.80900 number of atom coordinates read : 2442 total number of charged atoms : 2303 net assigned charge : 1.939008 assigned positive charge : 372.0587 centred at (gu) : 89.61413 87.58674 90.71714 assigned negative charge : -370.1205 centred at (gu) : 89.53716 87.70686 90.83997 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5372 nv = 96 ne = 84 npr = 49175 no. pairs analyzed = 49175 no. exposed pairs = 2956 no. arc points = 21161 no. surface atoms = 993 nbur = 1449 mkacc time = 0.1200000 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 = 1.484000 m= 212 mr = 2908 m= 0 mr = 16 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2166 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0115836E-09 -2.0609772E-09 midg,1,midg; midg,igrid,midg 4.1826094E-09 -9.4677510E-10 1,midg,midg; igrid,midg,midg -1.0382628E-09 1.4910778E-09 gauss-seidel spectral radius is 0.9844783 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 18:51:51 rms-change max change #iterations 8.8089108E-02 15.18347 at 10iterations 6.8622385E-03 1.056473 at 20iterations 5.4917904E-04 9.4676971E-02 at 30iterations 4.9720060E-05 9.7198486E-03 at 40iterations 5.9469917E-06 1.3389587E-03 at 50iterations finished qdiffx linear iterations at : 18:51:53 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 5.9469917E-06 1.3389587E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 18:51:54 3.595u 0.171s 0:04.17 90.1% 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 Mon Oct 10 2011 at 18:51:54 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: SEP 33 has a net charge of -0.4750 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: MG6 661 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.732501 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): 45.59600 104.0240 ymin,ymax (A): 8.777000 70.42200 zmin,zma (A): 19.98400 63.63400 x,y,z range (A): 58.42800 61.64500 43.65000 scale (grids/A): 1.732501 object centre (A): 74.81000 39.59950 41.80900 number of atom coordinates read : 2442 total number of charged atoms : 2303 net assigned charge : 1.939008 assigned positive charge : 372.0587 centred at (gu) : 88.84191 82.75964 92.15086 assigned negative charge : -370.1205 centred at (gu) : 88.61108 83.12039 92.51970 start vw surface at 0.2000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 58518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21161 grid for indexing accessible points = 1.400000 m= 19414 mr = 40414 m= 2244 mr = 14003 m= 76 mr = 1177 m= 0 mr = 16 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1036 time to turn everything in is 0.5100000 number of dielectric boundary points 24642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 17867 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) : 0.5775002 object centre at (A) : 74.81000 39.59950 41.80900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4063169E-03 -4.4108410E-03 midg,1,midg; midg,igrid,midg 1.5810883E-02 -1.6097690E-03 1,midg,midg; igrid,midg,midg -8.5848672E-03 1.7751222E-02 gauss-seidel spectral radius is 0.9983290 estimated iterations to convergence 194 setup time was (sec) 0.8100000 now iterating at: 18:51:55 rms-change max change #iterations 3.440364 187.4323 at 10iterations 1.475806 60.26382 at 20iterations 0.6366922 25.20319 at 30iterations 0.2754010 9.585045 at 40iterations 0.1187301 4.582352 at 50iterations 5.1425304E-02 2.023293 at 60iterations 2.2280401E-02 0.7627335 at 70iterations 9.6429409E-03 0.3432488 at 80iterations 4.1848561E-03 0.1727376 at 90iterations 1.8136655E-03 8.0003738E-02 at 100iterations 7.8341103E-04 2.9647350E-02 at 110iterations 3.4107498E-04 1.2266561E-02 at 120iterations finished qdiffx linear iterations at : 18:52:02 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 3.4107498E-04 1.2266561E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 18:52:03 7.901u 0.223s 0:08.85 91.7% 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 18:52:03 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: SEP 33 has a net charge of -0.4750 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: MG6 661 has a net charge of 1.4000 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: 2.598751 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): 45.59600 104.0240 ymin,ymax (A): 8.777000 70.42200 zmin,zma (A): 19.98400 63.63400 x,y,z range (A): 58.42800 61.64500 43.65000 scale (grids/A): 2.598751 object centre (A): 74.81000 39.59950 41.80900 number of atom coordinates read : 2442 total number of charged atoms : 2303 net assigned charge : 1.939008 assigned positive charge : 372.0587 centred at (gu) : 88.26279 79.13926 93.22618 assigned negative charge : -370.1205 centred at (gu) : 87.91660 79.68053 93.77957 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 135458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21161 grid for indexing accessible points = 1.400000 m= 64851 mr = 98013 m= 20661 mr = 52606 m= 3727 mr = 16146 m= 321 mr = 2572 m= 9 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 3531 time to turn everything in is 1.130000 number of dielectric boundary points 55531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 18419 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) : 1.732501 object centre at (A) : 74.81000 39.59950 41.80900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1171558 -4.4242401E-02 midg,1,midg; midg,igrid,midg 0.4168796 0.1909142 1,midg,midg; igrid,midg,midg -0.2129421 0.2941107 gauss-seidel spectral radius is 0.9991641 estimated iterations to convergence 273 setup time was (sec) 1.440000 now iterating at: 18:52:05 rms-change max change #iterations 8.518089 518.5128 at 10iterations 4.831497 114.7121 at 20iterations 2.706100 64.73460 at 30iterations 1.515662 32.87725 at 40iterations 0.8456737 19.45462 at 50iterations 0.4705979 10.66550 at 60iterations 0.2621982 5.648470 at 70iterations 0.1458279 2.943335 at 80iterations 8.0916531E-02 1.879959 at 90iterations 4.4900995E-02 0.9274120 at 100iterations 2.4897646E-02 0.5332031 at 110iterations 1.3841784E-02 0.2928200 at 120iterations 7.6588956E-03 0.1520357 at 130iterations 4.2535495E-03 8.5237503E-02 at 140iterations 2.3624750E-03 5.0218582E-02 at 150iterations 1.3072521E-03 2.8077126E-02 at 160iterations 7.2588993E-04 1.4974117E-02 at 170iterations 4.0367380E-04 8.4800720E-03 at 180iterations finished qdiffx linear iterations at : 18:52:18 total time elapsed so far: 14.39000 # loops : 180 mean,max change (kT/e) : 4.0367380E-04 8.4800720E-03 energy calculations done at 14.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.57000 DelPhi exited at 18:52:18 14.570u 0.231s 0:15.28 96.8% 0+0k 0+0io 0pf+0w