Sun Oct 9 03:48:42 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 Sun Oct 9 2011 at 03:48:42 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 = 5523 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5074551 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): -2.963000 64.49100 ymin,ymax (A): -10.99900 59.15500 zmin,zma (A): -19.81400 41.94200 x,y,z range (A): 67.45399 70.15400 61.75600 scale (grids/A): 0.5074551 object centre (A): 30.76400 24.07800 11.06400 number of atom coordinates read : 5523 total number of charged atoms : 5365 net assigned charge : 16.99996 assigned positive charge : 838.1572 centred at (gu) : 90.07468 92.10569 89.82092 assigned negative charge : -821.1652 centred at (gu) : 90.01096 92.14896 89.78704 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8377 nv = 96 ne = 84 npr = 114099 no. pairs analyzed = 114099 no. exposed pairs = 7409 no. arc points = 50238 no. surface atoms = 2475 nbur = 3048 mkacc time = 0.2500000 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 = 1.708000 m= 286 mr = 3911 m= 0 mr = 7 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4807 ## 697 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11736 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2850866E-10 2.8480487E-10 midg,1,midg; midg,igrid,midg 1.8716959E-10 1.6535080E-10 1,midg,midg; igrid,midg,midg 4.3898031E-11 3.8209497E-10 gauss-seidel spectral radius is 0.9801862 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 03:48:43 rms-change max change #iterations 7.2117478E-02 11.29334 at 10iterations 6.1802347E-03 0.8138161 at 20iterations 1.6384537E-03 0.2210960 at 30iterations 5.5290753E-04 6.8660736E-02 at 40iterations 1.9001125E-04 2.2388458E-02 at 50iterations finished qdiffx linear iterations at : 03:48:45 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.9001125E-04 2.2388458E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 03:48:46 3.332u 0.141s 0:03.84 90.3% 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 03:48:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5523 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.522365 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): -2.963000 64.49100 ymin,ymax (A): -10.99900 59.15500 zmin,zma (A): -19.81400 41.94200 x,y,z range (A): 67.45399 70.15400 61.75600 scale (grids/A): 1.522365 object centre (A): 30.76400 24.07800 11.06400 number of atom coordinates read : 5523 total number of charged atoms : 5365 net assigned charge : 16.99996 assigned positive charge : 838.1572 centred at (gu) : 90.22159 96.31471 89.46046 assigned negative charge : -821.1652 centred at (gu) : 90.03266 96.44624 89.36088 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 93089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50238 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 25644 mr = 59789 m= 2206 mr = 16082 m= 36 mr = 886 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 44216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 621 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 40287 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) : 0.5074551 object centre at (A) : 30.76400 24.07800 11.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2478390E-03 1.1523465E-02 midg,1,midg; midg,igrid,midg 3.2364011E-02 4.2420037E-02 1,midg,midg; igrid,midg,midg -9.9379150E-03 1.3371606E-02 gauss-seidel spectral radius is 0.9981526 estimated iterations to convergence 185 setup time was (sec) 0.9900000 now iterating at: 03:48:47 rms-change max change #iterations 4.053769 164.6167 at 10iterations 1.668042 49.27429 at 20iterations 0.6886772 22.68436 at 30iterations 0.2855261 9.391068 at 40iterations 0.1182141 3.734266 at 50iterations 4.9227290E-02 1.607834 at 60iterations 2.0792531E-02 0.6910191 at 70iterations 8.9899329E-03 0.2804604 at 80iterations 4.1149734E-03 0.1322021 at 90iterations 2.0812189E-03 6.7024231E-02 at 100iterations 1.1760342E-03 3.7757874E-02 at 110iterations 7.2526798E-04 2.4318695E-02 at 120iterations finished qdiffx linear iterations at : 03:48:54 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 7.2526798E-04 2.4318695E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 03:48:54 8.052u 0.246s 0:08.58 96.6% 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 Sun Oct 9 2011 at 03:48:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5523 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.283548 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): -2.963000 64.49100 ymin,ymax (A): -10.99900 59.15500 zmin,zma (A): -19.81400 41.94200 x,y,z range (A): 67.45399 70.15400 61.75600 scale (grids/A): 2.283548 object centre (A): 30.76400 24.07800 11.06400 number of atom coordinates read : 5523 total number of charged atoms : 5365 net assigned charge : 16.99996 assigned positive charge : 838.1572 centred at (gu) : 90.33182 99.47139 89.19028 assigned negative charge : -821.1652 centred at (gu) : 90.04879 99.66921 89.04103 start vw surface at 0.2000000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 216961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50238 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 90899 mr = 148943 m= 23114 mr = 67305 m= 3060 mr = 16312 m= 125 mr = 1765 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 99798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 42776 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) : 1.522365 object centre at (A) : 30.76400 24.07800 11.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2813928E-02 0.1716992 midg,1,midg; midg,igrid,midg 0.9151980 0.6505889 1,midg,midg; igrid,midg,midg -0.2584751 0.3053767 gauss-seidel spectral radius is 0.9991965 estimated iterations to convergence 279 setup time was (sec) 1.940000 now iterating at: 03:48:56 rms-change max change #iterations 11.19105 265.4837 at 10iterations 6.553331 160.0599 at 20iterations 3.803900 80.19507 at 30iterations 2.190111 52.00159 at 40iterations 1.255788 29.40797 at 50iterations 0.7178028 14.90503 at 60iterations 0.4078438 8.313869 at 70iterations 0.2314725 4.610682 at 80iterations 0.1313374 2.626892 at 90iterations 7.4273102E-02 1.502692 at 100iterations 4.1956045E-02 0.8874512 at 110iterations 2.3751741E-02 0.4817352 at 120iterations 1.3456560E-02 0.2447214 at 130iterations 7.6481639E-03 0.1482468 at 140iterations 4.3753576E-03 7.8155994E-02 at 150iterations 2.5306852E-03 4.6215057E-02 at 160iterations 1.4912401E-03 2.8299332E-02 at 170iterations 9.0151065E-04 1.6288757E-02 at 180iterations finished qdiffx linear iterations at : 03:49:08 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 9.0151065E-04 1.6288757E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 03:49:09 13.704u 0.272s 0:14.28 97.8% 0+0k 0+0io 0pf+0w