Tue Oct 11 06:11:47 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 06:11:47 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 = 2077 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: 0.7231069 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): 0.5159999 46.42000 ymin,ymax (A): 0.5749999 41.42700 zmin,zma (A): -2.019000 47.21300 x,y,z range (A): 45.90400 40.85200 49.23200 scale (grids/A): 0.7231069 object centre (A): 23.46800 21.00100 22.59700 number of atom coordinates read : 2077 total number of charged atoms : 1949 net assigned charge : 7.500009 assigned positive charge : 315.2170 centred at (gu) : 91.33677 90.29544 90.37604 assigned negative charge : -307.7172 centred at (gu) : 91.52486 90.28291 90.42409 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7495 nv = 96 ne = 84 npr = 41656 no. pairs analyzed = 41656 no. exposed pairs = 2493 no. arc points = 17038 no. surface atoms = 849 nbur = 1228 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 524 mr = 4421 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1562 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8016 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1718862E-07 6.4046617E-08 midg,1,midg; midg,igrid,midg 7.9934182E-08 1.0725694E-07 1,midg,midg; igrid,midg,midg 1.7038745E-07 -5.1804999E-08 gauss-seidel spectral radius is 0.9900261 estimated iterations to convergence 81 setup time was (sec) 0.4800000 now iterating at: 06:11:48 rms-change max change #iterations 0.2179245 34.10186 at 10iterations 2.9103316E-02 5.014236 at 20iterations 3.9731986E-03 0.5678291 at 30iterations 7.1637006E-04 8.7228775E-02 at 40iterations 1.9676775E-04 2.7523518E-02 at 50iterations finished qdiffx linear iterations at : 06:11:50 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 1.9676775E-04 2.7523518E-02 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 06:11:51 3.059u 0.143s 0:03.56 89.6% 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 Tue Oct 11 2011 at 06:11:51 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 = 2077 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: 2.169321 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): 0.5159999 46.42000 ymin,ymax (A): 0.5749999 41.42700 zmin,zma (A): -2.019000 47.21300 x,y,z range (A): 45.90400 40.85200 49.23200 scale (grids/A): 2.169321 object centre (A): 23.46800 21.00100 22.59700 number of atom coordinates read : 2077 total number of charged atoms : 1949 net assigned charge : 7.500009 assigned positive charge : 315.2170 centred at (gu) : 94.01022 90.88646 91.12836 assigned negative charge : -307.7172 centred at (gu) : 94.57466 90.84866 91.27214 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17038 grid for indexing accessible points = 1.400000 m= 32761 mr = 56902 m= 6637 mr = 25293 m= 621 mr = 4573 m= 7 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 31960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15488 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) : 0.7231069 object centre at (A) : 23.46800 21.00100 22.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1334360E-02 6.8048269E-02 midg,1,midg; midg,igrid,midg 6.7260228E-03 3.5840787E-02 1,midg,midg; igrid,midg,midg 4.2483214E-02 -8.6051301E-04 gauss-seidel spectral radius is 0.9988728 estimated iterations to convergence 236 setup time was (sec) 0.8400000 now iterating at: 06:11:52 rms-change max change #iterations 4.779901 267.0644 at 10iterations 2.401740 84.86156 at 20iterations 1.208401 34.38501 at 30iterations 0.6091343 18.09042 at 40iterations 0.3060698 8.633152 at 50iterations 0.1543595 4.340574 at 60iterations 7.7744536E-02 2.244221 at 70iterations 3.9300513E-02 1.172764 at 80iterations 1.9803124E-02 0.6186972 at 90iterations 1.0105717E-02 0.2852325 at 100iterations 5.1291417E-03 0.1524963 at 110iterations 2.6547464E-03 8.1806183E-02 at 120iterations finished qdiffx linear iterations at : 06:11:58 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 2.6547464E-03 8.1806183E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 06:11:58 6.957u 0.156s 0:07.42 95.6% 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 Tue Oct 11 2011 at 06:11:58 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 = 2077 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: 3.253981 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): 0.5159999 46.42000 ymin,ymax (A): 0.5749999 41.42700 zmin,zma (A): -2.019000 47.21300 x,y,z range (A): 45.90400 40.85200 49.23200 scale (grids/A): 3.253981 object centre (A): 23.46800 21.00100 22.59700 number of atom coordinates read : 2077 total number of charged atoms : 1949 net assigned charge : 7.500009 assigned positive charge : 315.2170 centred at (gu) : 96.01529 91.32961 91.69253 assigned negative charge : -307.7172 centred at (gu) : 96.86194 91.27294 91.90832 start vw surface at 0.1300000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 182077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17038 grid for indexing accessible points = 1.400000 m= 101177 mr = 136473 m= 42422 mr = 85052 m= 12684 mr = 35475 m= 2570 mr = 9940 m= 272 mr = 1932 m= 12 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 72183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 15592 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) : 2.169321 object centre at (A) : 23.46800 21.00100 22.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5231874 0.7641277 midg,1,midg; midg,igrid,midg -9.1394149E-03 0.2773125 1,midg,midg; igrid,midg,midg 0.2988870 0.1558454 gauss-seidel spectral radius is 0.9993047 estimated iterations to convergence 299 setup time was (sec) 2.040000 now iterating at: 06:12:00 rms-change max change #iterations 10.54920 486.1396 at 10iterations 6.278564 187.4005 at 20iterations 3.717749 78.07048 at 30iterations 2.201289 42.68852 at 40iterations 1.300667 27.02107 at 50iterations 0.7659601 15.34948 at 60iterations 0.4522007 8.677500 at 70iterations 0.2658281 5.036071 at 80iterations 0.1566559 2.912215 at 90iterations 9.1999546E-02 1.608688 at 100iterations 5.4213058E-02 1.054897 at 110iterations 3.1982090E-02 0.5669293 at 120iterations 1.8938296E-02 0.3171024 at 130iterations 1.1357873E-02 0.1925583 at 140iterations 6.9400780E-03 0.1220894 at 150iterations 4.3731052E-03 7.5222015E-02 at 160iterations 2.9044647E-03 4.9526215E-02 at 170iterations 2.0577330E-03 3.3508301E-02 at 180iterations finished qdiffx linear iterations at : 06:12:10 total time elapsed so far: 11.50000 # loops : 180 mean,max change (kT/e) : 2.0577330E-03 3.3508301E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 06:12:10 11.690u 0.177s 0:12.34 96.1% 0+0k 0+0io 0pf+0w