Tue Oct 11 08:33:05 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 08:33:05 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 = 2364 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: 0.6331478 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): -9.044000 36.33600 ymin,ymax (A): -15.39300 40.83400 zmin,zma (A): 5.426000 52.57000 x,y,z range (A): 45.38000 56.22700 47.14400 scale (grids/A): 0.6331478 object centre (A): 13.64600 12.72050 28.99800 number of atom coordinates read : 2364 total number of charged atoms : 2228 net assigned charge : 4.500007 assigned positive charge : 353.9043 centred at (gu) : 90.55725 89.02145 90.55305 assigned negative charge : -349.4048 centred at (gu) : 90.47704 89.02294 90.69711 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6435 nv = 96 ne = 84 npr = 47565 no. pairs analyzed = 47565 no. exposed pairs = 2860 no. arc points = 20154 no. surface atoms = 980 nbur = 1384 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 332 mr = 3618 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2092 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5727595E-08 -8.2955367E-09 midg,1,midg; midg,igrid,midg 6.8026900E-09 4.3095287E-09 1,midg,midg; igrid,midg,midg -1.4021081E-09 1.3888191E-08 gauss-seidel spectral radius is 0.9870564 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 08:33:05 rms-change max change #iterations 0.1334593 21.48528 at 10iterations 1.2903314E-02 2.363388 at 20iterations 1.3459199E-03 0.1932583 at 30iterations 1.6806179E-04 2.9571533E-02 at 40iterations 2.6643267E-05 4.1198730E-03 at 50iterations finished qdiffx linear iterations at : 08:33:09 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 2.6643267E-05 4.1198730E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 08:33:09 4.188u 0.176s 0:04.67 93.1% 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 Oct 11 2011 at 08:33:09 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 = 2364 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: 1.899443 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): -9.044000 36.33600 ymin,ymax (A): -15.39300 40.83400 zmin,zma (A): 5.426000 52.57000 x,y,z range (A): 45.38000 56.22700 47.14400 scale (grids/A): 1.899443 object centre (A): 13.64600 12.72050 28.99800 number of atom coordinates read : 2364 total number of charged atoms : 2228 net assigned charge : 4.500007 assigned positive charge : 353.9043 centred at (gu) : 91.67152 87.06421 91.65869 assigned negative charge : -349.4048 centred at (gu) : 91.43111 87.06878 92.09113 start vw surface at 0.2400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 69313 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20154 grid for indexing accessible points = 1.400000 m= 25176 mr = 48617 m= 3745 mr = 18695 m= 226 mr = 2272 m= 4 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 537 time to turn everything in is 0.7200000 number of dielectric boundary points 28772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 17516 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) : 0.6331478 object centre at (A) : 13.64600 12.72050 28.99800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2788567E-02 -2.0797892E-02 midg,1,midg; midg,igrid,midg 1.6001809E-02 3.2657377E-02 1,midg,midg; igrid,midg,midg -3.5038281E-03 7.7955020E-03 gauss-seidel spectral radius is 0.9986050 estimated iterations to convergence 212 setup time was (sec) 1.060000 now iterating at: 08:33:11 rms-change max change #iterations 3.963754 179.9598 at 10iterations 1.853256 62.31676 at 20iterations 0.8657792 26.86431 at 30iterations 0.4021952 13.52967 at 40iterations 0.1873759 6.034737 at 50iterations 8.7334640E-02 2.822344 at 60iterations 4.0739622E-02 1.480964 at 70iterations 1.8912572E-02 0.6323428 at 80iterations 8.7934807E-03 0.3037481 at 90iterations 4.0940507E-03 0.1380825 at 100iterations 1.9061945E-03 6.2839985E-02 at 110iterations 8.9137285E-04 3.2825470E-02 at 120iterations finished qdiffx linear iterations at : 08:33:19 total time elapsed so far: 9.290000 # loops : 120 mean,max change (kT/e) : 8.9137285E-04 3.2825470E-02 energy calculations done at 9.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 08:33:20 9.527u 0.203s 0:10.22 95.1% 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 Oct 11 2011 at 08:33:20 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 = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.849165 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): -9.044000 36.33600 ymin,ymax (A): -15.39300 40.83400 zmin,zma (A): 5.426000 52.57000 x,y,z range (A): 45.38000 56.22700 47.14400 scale (grids/A): 2.849165 object centre (A): 13.64600 12.72050 28.99800 number of atom coordinates read : 2364 total number of charged atoms : 2228 net assigned charge : 4.500007 assigned positive charge : 353.9043 centred at (gu) : 92.50709 85.59622 92.48802 assigned negative charge : -349.4048 centred at (gu) : 92.14658 85.60310 93.13671 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 159857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20154 grid for indexing accessible points = 1.400000 m= 82401 mr = 117190 m= 28932 mr = 67947 m= 6724 mr = 23283 m= 1007 mr = 4995 m= 66 mr = 709 m= 0 mr = 32 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 1852 time to turn everything in is 1.580000 number of dielectric boundary points 64831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 17821 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) : 1.899443 object centre at (A) : 13.64600 12.72050 28.99800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3747738 -0.2845665 midg,1,midg; midg,igrid,midg 0.1450932 0.3305229 1,midg,midg; igrid,midg,midg -2.0059917E-02 1.6993620E-02 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.930000 now iterating at: 08:33:22 rms-change max change #iterations 9.359853 335.2863 at 10iterations 5.431378 121.6987 at 20iterations 3.129563 80.41154 at 30iterations 1.800324 37.13220 at 40iterations 1.033654 19.62250 at 50iterations 0.5937817 11.31045 at 60iterations 0.3396016 7.248352 at 70iterations 0.1946947 3.583108 at 80iterations 0.1110894 2.166607 at 90iterations 6.3643120E-02 1.174229 at 100iterations 3.6348958E-02 0.7032166 at 110iterations 2.0733839E-02 0.3870487 at 120iterations 1.1840625E-02 0.2205992 at 130iterations 6.7876107E-03 0.1244560 at 140iterations 3.8723468E-03 7.1054459E-02 at 150iterations 2.2252908E-03 4.8407555E-02 at 160iterations 1.2783166E-03 2.3365021E-02 at 170iterations 7.3808728E-04 1.4045715E-02 at 180iterations finished qdiffx linear iterations at : 08:33:34 total time elapsed so far: 14.53000 # loops : 180 mean,max change (kT/e) : 7.3808728E-04 1.4045715E-02 energy calculations done at 14.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.77000 DelPhi exited at 08:33:35 14.776u 0.207s 0:15.73 95.1% 0+0k 0+0io 0pf+0w