Tue Oct 11 06:49:20 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 Tue Oct 11 2011 at 06:49:20 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 = 2946 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: 0.5721541 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): -16.88000 45.34100 ymin,ymax (A): 21.94000 79.21900 zmin,zma (A): -71.25900 -23.21900 x,y,z range (A): 62.22100 57.27900 48.04000 scale (grids/A): 0.5721541 object centre (A): 14.23050 50.57950 -47.23900 number of atom coordinates read : 2946 total number of charged atoms : 2806 net assigned charge : -2.499990 assigned positive charge : 428.1136 centred at (gu) : 88.56563 89.61839 89.54077 assigned negative charge : -430.6142 centred at (gu) : 88.51392 89.72399 89.53396 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6401 nv = 96 ne = 84 npr = 60730 no. pairs analyzed = 60730 no. exposed pairs = 3705 no. arc points = 25665 no. surface atoms = 1259 nbur = 1687 mkacc time = 0.1300000 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= 321 mr = 3482 m= 2 mr = 20 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 0.3600000 number of dielectric boundary points 3222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2554 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8122 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7506017E-10 -2.6531172E-10 midg,1,midg; midg,igrid,midg 1.4265675E-09 -1.9661590E-09 1,midg,midg; igrid,midg,midg -1.7711822E-09 3.0350392E-10 gauss-seidel spectral radius is 0.9842367 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 06:49:21 rms-change max change #iterations 9.1328450E-02 16.06010 at 10iterations 7.0470334E-03 1.161636 at 20iterations 6.5444165E-04 0.1110115 at 30iterations 1.1556326E-04 2.7772903E-02 at 40iterations 2.9334211E-05 7.3928833E-03 at 50iterations finished qdiffx linear iterations at : 06:49:24 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 2.9334211E-05 7.3928833E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 06:49:25 4.314u 0.188s 0:05.03 89.2% 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 06:49:25 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 = 2946 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: 1.716462 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): -16.88000 45.34100 ymin,ymax (A): 21.94000 79.21900 zmin,zma (A): -71.25900 -23.21900 x,y,z range (A): 62.22100 57.27900 48.04000 scale (grids/A): 1.716462 object centre (A): 14.23050 50.57950 -47.23900 number of atom coordinates read : 2946 total number of charged atoms : 2806 net assigned charge : -2.499990 assigned positive charge : 428.1136 centred at (gu) : 85.69636 88.85465 88.62163 assigned negative charge : -430.6142 centred at (gu) : 85.54169 89.17146 88.60177 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25665 grid for indexing accessible points = 1.400000 m= 23819 mr = 47745 m= 3095 mr = 17174 m= 123 mr = 1812 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 29759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21733 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) : 0.5721541 object centre at (A) : 14.23050 50.57950 -47.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0938218E-02 1.0167976E-02 midg,1,midg; midg,igrid,midg -4.8072166E-03 1.0827192E-02 1,midg,midg; igrid,midg,midg -3.2465059E-02 -2.8108306E-02 gauss-seidel spectral radius is 0.9983622 estimated iterations to convergence 196 setup time was (sec) 0.7900000 now iterating at: 06:49:26 rms-change max change #iterations 3.621523 151.8652 at 10iterations 1.578162 58.51610 at 20iterations 0.6848478 24.24315 at 30iterations 0.2997259 10.52308 at 40iterations 0.1300350 5.068794 at 50iterations 5.7087101E-02 1.982327 at 60iterations 2.4788324E-02 0.8946838 at 70iterations 1.0864985E-02 0.3616714 at 80iterations 4.7713066E-03 0.1825027 at 90iterations 2.0978744E-03 8.2054138E-02 at 100iterations 9.3199773E-04 3.3507347E-02 at 110iterations 4.2349752E-04 1.5171051E-02 at 120iterations finished qdiffx linear iterations at : 06:49:32 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 4.2349752E-04 1.5171051E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 06:49:33 6.968u 0.173s 0:07.55 94.4% 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 06:49:33 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 = 2946 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: 2.574693 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): -16.88000 45.34100 ymin,ymax (A): 21.94000 79.21900 zmin,zma (A): -71.25900 -23.21900 x,y,z range (A): 62.22100 57.27900 48.04000 scale (grids/A): 2.574693 object centre (A): 14.23050 50.57950 -47.23900 number of atom coordinates read : 2946 total number of charged atoms : 2806 net assigned charge : -2.499990 assigned positive charge : 428.1136 centred at (gu) : 83.54433 88.28188 87.93217 assigned negative charge : -430.6142 centred at (gu) : 83.31242 88.75726 87.90259 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 161211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25665 grid for indexing accessible points = 1.400000 m= 78590 mr = 116177 m= 26315 mr = 63687 m= 5265 mr = 20875 m= 526 mr = 3734 m= 11 mr = 315 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 67130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 22437 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) : 1.716462 object centre at (A) : 14.23050 50.57950 -47.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1914972 0.1533724 midg,1,midg; midg,igrid,midg -5.3109881E-02 0.1862938 1,midg,midg; igrid,midg,midg -0.4614451 -0.6073688 gauss-seidel spectral radius is 0.9991955 estimated iterations to convergence 278 setup time was (sec) 1.580000 now iterating at: 06:49:35 rms-change max change #iterations 9.088318 273.2367 at 10iterations 5.180211 126.4420 at 20iterations 2.940402 76.90042 at 30iterations 1.665417 37.40304 at 40iterations 0.9409241 19.61219 at 50iterations 0.5306116 10.10114 at 60iterations 0.2988147 5.860457 at 70iterations 0.1680263 3.235550 at 80iterations 9.4294019E-02 1.724659 at 90iterations 5.2922789E-02 1.099758 at 100iterations 2.9674109E-02 0.5387211 at 110iterations 1.6640959E-02 0.3217945 at 120iterations 9.3578845E-03 0.1809845 at 130iterations 5.2342312E-03 0.1003952 at 140iterations 2.9382852E-03 5.6365013E-02 at 150iterations 1.6466547E-03 3.2730103E-02 at 160iterations 9.2432374E-04 1.8476486E-02 at 170iterations 5.2008097E-04 9.4413757E-03 at 180iterations finished qdiffx linear iterations at : 06:49:44 total time elapsed so far: 11.20000 # loops : 180 mean,max change (kT/e) : 5.2008097E-04 9.4413757E-03 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.41000 DelPhi exited at 06:49:46 11.414u 0.234s 0:13.06 89.1% 0+0k 0+0io 0pf+0w