Sun Oct 9 11:11:58 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 Sun Oct 9 2011 at 11:11:58 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2880 !!! WARNING: HIR 212 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5846993 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): -20.50700 40.37900 ymin,ymax (A): -29.52700 29.27500 zmin,zma (A): 1.153000 55.84600 x,y,z range (A): 60.88600 58.80200 54.69300 scale (grids/A): 0.5846993 object centre (A): 9.935999 -0.1260004 28.49950 number of atom coordinates read : 2880 total number of charged atoms : 2809 net assigned charge : 6.514018 assigned positive charge : 435.1470 centred at (gu) : 90.56273 91.15997 88.97352 assigned negative charge : -428.6348 centred at (gu) : 90.56079 91.17126 89.05446 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6792 nv = 96 ne = 84 npr = 54606 no. pairs analyzed = 54606 no. exposed pairs = 4123 no. arc points = 28888 no. surface atoms = 1361 nbur = 1519 mkacc time = 0.1000000 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= 377 mr = 3346 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2910 ## 318 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8618 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6116937E-09 -2.7428704E-10 midg,1,midg; midg,igrid,midg 1.4859185E-09 1.7773391E-09 1,midg,midg; igrid,midg,midg 1.4128410E-09 1.9283533E-09 gauss-seidel spectral radius is 0.9849083 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 11:11:59 rms-change max change #iterations 9.8903239E-02 16.91804 at 10iterations 7.8280577E-03 1.183483 at 20iterations 7.0925721E-04 9.8487854E-02 at 30iterations 9.8479693E-05 1.4610291E-02 at 40iterations 2.1395743E-05 2.6130676E-03 at 50iterations finished qdiffx linear iterations at : 11:12:02 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.1395743E-05 2.6130676E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 11:12:02 3.421u 0.184s 0:04.05 88.8% 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 11:12:02 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2880 !!! WARNING: HIR 212 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.754098 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): -20.50700 40.37900 ymin,ymax (A): -29.52700 29.27500 zmin,zma (A): 1.153000 55.84600 x,y,z range (A): 60.88600 58.80200 54.69300 scale (grids/A): 1.754098 object centre (A): 9.935999 -0.1260004 28.49950 number of atom coordinates read : 2880 total number of charged atoms : 2809 net assigned charge : 6.514018 assigned positive charge : 435.1470 centred at (gu) : 91.68716 93.47920 86.91974 assigned negative charge : -428.6348 centred at (gu) : 91.68204 93.51376 87.16321 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28888 grid for indexing accessible points = 1.400000 m= 24240 mr = 48885 m= 3397 mr = 16393 m= 143 mr = 1819 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 162 time to turn everything in is 0.3700000 number of dielectric boundary points 34906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 21909 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) : 0.5846993 object centre at (A) : 9.935999 -0.1260004 28.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1750719E-02 -5.0070491E-03 midg,1,midg; midg,igrid,midg 2.2985615E-02 3.2628838E-02 1,midg,midg; igrid,midg,midg -6.6395043E-03 1.5536445E-02 gauss-seidel spectral radius is 0.9984514 estimated iterations to convergence 202 setup time was (sec) 0.5900000 now iterating at: 11:12:03 rms-change max change #iterations 3.822164 186.7208 at 10iterations 1.690071 67.43589 at 20iterations 0.7513584 25.41147 at 30iterations 0.3360247 10.99595 at 40iterations 0.1490873 5.241535 at 50iterations 6.6325575E-02 2.049522 at 60iterations 2.9482719E-02 0.9363403 at 70iterations 1.3151933E-02 0.4297867 at 80iterations 5.8802981E-03 0.2042456 at 90iterations 2.6278144E-03 0.1013765 at 100iterations 1.1799723E-03 3.8664937E-02 at 110iterations 5.3227076E-04 1.8021584E-02 at 120iterations finished qdiffx linear iterations at : 11:12:10 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 5.3227076E-04 1.8021584E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 11:12:11 7.828u 0.196s 0:08.39 95.4% 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 Sun Oct 9 2011 at 11:12:11 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2880 !!! WARNING: HIR 212 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.631147 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): -20.50700 40.37900 ymin,ymax (A): -29.52700 29.27500 zmin,zma (A): 1.153000 55.84600 x,y,z range (A): 60.88600 58.80200 54.69300 scale (grids/A): 2.631147 object centre (A): 9.935999 -0.1260004 28.49950 number of atom coordinates read : 2880 total number of charged atoms : 2809 net assigned charge : 6.514018 assigned positive charge : 435.1470 centred at (gu) : 92.53060 95.21867 85.37936 assigned negative charge : -428.6348 centred at (gu) : 92.52306 95.27068 85.74473 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 172013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28888 grid for indexing accessible points = 1.400000 m= 80264 mr = 120102 m= 26437 mr = 62064 m= 5726 mr = 19856 m= 605 mr = 3899 m= 17 mr = 302 m= 0 mr = 4 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 495 time to turn everything in is 0.9300000 number of dielectric boundary points 78835 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 22462 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) : 1.754098 object centre at (A) : 9.935999 -0.1260004 28.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1557154 -4.9229991E-02 midg,1,midg; midg,igrid,midg 0.2813353 0.4706763 1,midg,midg; igrid,midg,midg -0.1462175 0.3235716 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 1.160000 now iterating at: 11:12:12 rms-change max change #iterations 9.644522 257.2672 at 10iterations 5.702900 144.2805 at 20iterations 3.327565 88.98251 at 30iterations 1.925069 38.64698 at 40iterations 1.110705 23.71952 at 50iterations 0.6386884 13.49167 at 60iterations 0.3665575 7.348466 at 70iterations 0.2094187 3.966079 at 80iterations 0.1197243 2.390301 at 90iterations 6.8279125E-02 1.326038 at 100iterations 3.8911954E-02 0.8532333 at 110iterations 2.2120638E-02 0.4608765 at 120iterations 1.2616000E-02 0.2353117 at 130iterations 7.1727256E-03 0.1320724 at 140iterations 4.0950491E-03 7.9048157E-02 at 150iterations 2.3256531E-03 4.3151855E-02 at 160iterations 1.3256676E-03 2.6882172E-02 at 170iterations 7.5396604E-04 1.5386581E-02 at 180iterations finished qdiffx linear iterations at : 11:12:24 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 7.5396604E-04 1.5386581E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 11:12:24 12.695u 0.209s 0:13.27 97.1% 0+0k 0+0io 0pf+0w