Tue Nov 22 14:10:52 PST 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 Nov 22 2011 at 14:10:57 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 = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6251097 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): -35.21400 9.832000 ymin,ymax (A): 1.186000 42.74900 zmin,zma (A): -0.2710000 56.67900 x,y,z range (A): 45.04600 41.56300 56.95000 scale (grids/A): 0.6251097 object centre (A): -12.69100 21.96750 28.20400 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8221 centred at (gu) : 90.47780 89.09566 89.79984 assigned negative charge : -284.8223 centred at (gu) : 90.39970 89.24985 89.81626 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5244 nv = 96 ne = 84 npr = 39831 no. pairs analyzed = 39831 no. exposed pairs = 2496 no. arc points = 17157 no. surface atoms = 850 nbur = 1110 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 2893 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6165 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7979992E-09 1.7119426E-09 midg,1,midg; midg,igrid,midg 1.3773034E-08 -5.0074962E-09 1,midg,midg; igrid,midg,midg -1.5489671E-09 7.8685449E-09 gauss-seidel spectral radius is 0.9866912 estimated iterations to convergence 71 setup time was (sec) 0.4500000 now iterating at: 14:11:00 rms-change max change #iterations 0.1090351 19.06301 at 10iterations 1.0316152E-02 1.566113 at 20iterations 9.4472384E-04 0.1631870 at 30iterations 8.9471039E-05 1.4511108E-02 at 40iterations 8.1880389E-06 1.3275146E-03 at 50iterations finished qdiffx linear iterations at : 14:11:08 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 8.1880389E-06 1.3275146E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 14:11:10 3.186u 0.158s 0:13.25 25.1% 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 Tue Nov 22 2011 at 14:11:10 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 = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.875329 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): -35.21400 9.832000 ymin,ymax (A): 1.186000 42.74900 zmin,zma (A): -0.2710000 56.67900 x,y,z range (A): 45.04600 41.56300 56.95000 scale (grids/A): 1.875329 object centre (A): -12.69100 21.96750 28.20400 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8221 centred at (gu) : 91.43346 87.28712 89.39989 assigned negative charge : -284.8223 centred at (gu) : 91.19921 87.74989 89.44899 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 56231 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17157 grid for indexing accessible points = 1.400000 m= 20817 mr = 38667 m= 3332 mr = 15703 m= 199 mr = 2218 m= 1 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 23898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14377 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) : 0.6251097 object centre at (A) : -12.69100 21.96750 28.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8962188E-02 2.4830313E-02 midg,1,midg; midg,igrid,midg 8.0381297E-03 -6.9693727E-03 1,midg,midg; igrid,midg,midg -4.4703260E-03 -1.5059245E-03 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 0.6800000 now iterating at: 14:11:12 rms-change max change #iterations 3.435385 165.7482 at 10iterations 1.553501 63.77240 at 20iterations 0.7066954 25.87180 at 30iterations 0.3196329 12.37140 at 40iterations 0.1451883 5.307747 at 50iterations 6.5698393E-02 2.439898 at 60iterations 2.9837178E-02 1.080658 at 70iterations 1.3502619E-02 0.4722824 at 80iterations 6.1353780E-03 0.2430024 at 90iterations 2.7856166E-03 0.1031818 at 100iterations 1.2610486E-03 4.3954849E-02 at 110iterations 5.7571562E-04 2.2741556E-02 at 120iterations finished qdiffx linear iterations at : 14:11:25 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 5.7571562E-04 2.2741556E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 14:11:29 7.051u 0.184s 0:19.40 37.2% 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 Nov 22 2011 at 14:11:33 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 = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.812994 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): -35.21400 9.832000 ymin,ymax (A): 1.186000 42.74900 zmin,zma (A): -0.2710000 56.67900 x,y,z range (A): 45.04600 41.56300 56.95000 scale (grids/A): 2.812994 object centre (A): -12.69100 21.96750 28.20400 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8221 centred at (gu) : 92.15022 85.93080 89.09995 assigned negative charge : -284.8223 centred at (gu) : 91.79900 86.62478 89.17353 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 129629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17157 grid for indexing accessible points = 1.400000 m= 66551 mr = 93075 m= 24906 mr = 55124 m= 6167 mr = 20642 m= 859 mr = 4841 m= 48 mr = 650 m= 0 mr = 24 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 53804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 14623 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) : 1.875329 object centre at (A) : -12.69100 21.96750 28.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1955649E-02 0.1677188 midg,1,midg; midg,igrid,midg 6.9628456E-03 -8.7177895E-02 1,midg,midg; igrid,midg,midg -8.5766174E-02 -5.1393393E-02 gauss-seidel spectral radius is 0.9992098 estimated iterations to convergence 281 setup time was (sec) 1.330000 now iterating at: 14:11:40 rms-change max change #iterations 8.151574 327.3343 at 10iterations 4.651344 132.2254 at 20iterations 2.631281 78.16462 at 30iterations 1.487977 34.60852 at 40iterations 0.8396053 19.84640 at 50iterations 0.4735168 10.19556 at 60iterations 0.2655355 6.157990 at 70iterations 0.1500503 3.073485 at 80iterations 8.4491037E-02 1.755609 at 90iterations 4.7435224E-02 1.059351 at 100iterations 2.6750635E-02 0.6206417 at 110iterations 1.5043342E-02 0.3041534 at 120iterations 8.4580611E-03 0.1690521 at 130iterations 4.7661494E-03 0.1218700 at 140iterations 2.6779859E-03 5.4973602E-02 at 150iterations 1.5115332E-03 3.5846710E-02 at 160iterations 8.5063465E-04 1.7514706E-02 at 170iterations 4.7904186E-04 9.8781586E-03 at 180iterations finished qdiffx linear iterations at : 14:12:11 total time elapsed so far: 11.82000 # loops : 180 mean,max change (kT/e) : 4.7904186E-04 9.8781586E-03 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 14:12:13 11.997u 0.206s 0:40.03 30.4% 0+0k 0+0io 0pf+0w