Mon Oct 10 16:11:20 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 Mon Oct 10 2011 at 16:11:20 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3636 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 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: 0.5735737 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): -17.72100 31.47000 ymin,ymax (A): -32.40300 29.66400 zmin,zma (A): -25.90100 35.62400 x,y,z range (A): 49.19100 62.06700 61.52500 scale (grids/A): 0.5735737 object centre (A): 6.874499 -1.369500 4.861501 number of atom coordinates read : 3636 total number of charged atoms : 3531 net assigned charge : 4.700007 assigned positive charge : 539.0577 centred at (gu) : 90.72276 89.86091 88.69004 assigned negative charge : -534.3601 centred at (gu) : 90.78423 89.93342 88.62147 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8110 nv = 96 ne = 84 npr = 72609 no. pairs analyzed = 72609 no. exposed pairs = 4702 no. arc points = 32472 no. surface atoms = 1592 nbur = 2044 mkacc time = 0.1900000 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= 425 mr = 4373 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.4100000 number of dielectric boundary points 4121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3288 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7445307E-10 1.6882449E-09 midg,1,midg; midg,igrid,midg 2.4580480E-09 -6.8385730E-10 1,midg,midg; igrid,midg,midg 1.8113760E-09 -5.6784205E-10 gauss-seidel spectral radius is 0.9843737 estimated iterations to convergence 66 setup time was (sec) 0.7000000 now iterating at: 16:11:21 rms-change max change #iterations 0.1067260 15.60482 at 10iterations 8.1880679E-03 1.390168 at 20iterations 7.0993928E-04 0.1036758 at 30iterations 1.0627162E-04 1.3772011E-02 at 40iterations 2.8111603E-05 4.2220354E-03 at 50iterations finished qdiffx linear iterations at : 16:11:25 total time elapsed so far: 4.580000 # loops : 50 mean,max change (kT/e) : 2.8111603E-05 4.2220354E-03 energy calculations done at 4.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 16:11:25 4.758u 0.388s 0:05.42 94.6% 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 Mon Oct 10 2011 at 16:11:25 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3636 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 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: 1.720721 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): -17.72100 31.47000 ymin,ymax (A): -32.40300 29.66400 zmin,zma (A): -25.90100 35.62400 x,y,z range (A): 49.19100 62.06700 61.52500 scale (grids/A): 1.720721 object centre (A): 6.874499 -1.369500 4.861501 number of atom coordinates read : 3636 total number of charged atoms : 3531 net assigned charge : 4.700007 assigned positive charge : 539.0577 centred at (gu) : 92.16725 89.58177 86.06870 assigned negative charge : -534.3601 centred at (gu) : 92.35239 89.80013 85.86439 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32472 grid for indexing accessible points = 1.400000 m= 30983 mr = 61645 m= 4097 mr = 22243 m= 170 mr = 2251 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 518 time to turn everything in is 0.7300000 number of dielectric boundary points 38029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 27394 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) : 0.5735737 object centre at (A) : 6.874499 -1.369500 4.861501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3938576E-02 -3.2134468E-03 midg,1,midg; midg,igrid,midg 2.9686388E-02 1.3131924E-02 1,midg,midg; igrid,midg,midg -5.0469616E-04 -2.1231201E-04 gauss-seidel spectral radius is 0.9984520 estimated iterations to convergence 202 setup time was (sec) 1.040000 now iterating at: 16:11:27 rms-change max change #iterations 4.152939 169.9627 at 10iterations 1.848173 72.16276 at 20iterations 0.8225470 29.99215 at 30iterations 0.3664612 11.46733 at 40iterations 0.1639198 4.853760 at 50iterations 7.3302053E-02 2.932343 at 60iterations 3.2685500E-02 1.081881 at 70iterations 1.4602521E-02 0.4829407 at 80iterations 6.5408205E-03 0.1952238 at 90iterations 2.9269757E-03 8.3875656E-02 at 100iterations 1.3183675E-03 4.1526794E-02 at 110iterations 5.9741444E-04 1.7822266E-02 at 120iterations finished qdiffx linear iterations at : 16:11:37 total time elapsed so far: 10.94000 # loops : 120 mean,max change (kT/e) : 5.9741444E-04 1.7822266E-02 energy calculations done at 10.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 16:11:37 11.110u 0.436s 0:11.80 97.7% 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 Mon Oct 10 2011 at 16:11:37 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3636 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 has a net charge of 1.4000 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: 2.581082 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): -17.72100 31.47000 ymin,ymax (A): -32.40300 29.66400 zmin,zma (A): -25.90100 35.62400 x,y,z range (A): 49.19100 62.06700 61.52500 scale (grids/A): 2.581082 object centre (A): 6.874499 -1.369500 4.861501 number of atom coordinates read : 3636 total number of charged atoms : 3531 net assigned charge : 4.700007 assigned positive charge : 539.0577 centred at (gu) : 93.25061 89.37230 84.10284 assigned negative charge : -534.3601 centred at (gu) : 93.52847 89.70007 83.79652 start vw surface at 0.1500000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 206034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32472 grid for indexing accessible points = 1.400000 m= 102697 mr = 150086 m= 33921 mr = 82584 m= 6886 mr = 26496 m= 753 mr = 4851 m= 18 mr = 428 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 1814 time to turn everything in is 1.870000 number of dielectric boundary points 85864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 28234 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) : 1.720721 object centre at (A) : 6.874499 -1.369500 4.861501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4712084 -0.1164031 midg,1,midg; midg,igrid,midg 0.3477365 0.3498407 1,midg,midg; igrid,midg,midg -4.7592983E-02 6.0902010E-03 gauss-seidel spectral radius is 0.9992390 estimated iterations to convergence 286 setup time was (sec) 2.230000 now iterating at: 16:11:40 rms-change max change #iterations 10.32328 315.7592 at 10iterations 6.057152 135.2378 at 20iterations 3.530201 74.26788 at 30iterations 2.056885 39.81976 at 40iterations 1.187086 22.92194 at 50iterations 0.6858912 12.95965 at 60iterations 0.3950259 7.110833 at 70iterations 0.2278503 4.049078 at 80iterations 0.1305692 2.481701 at 90iterations 7.5076222E-02 1.294136 at 100iterations 4.2998973E-02 0.7922707 at 110iterations 2.4592470E-02 0.4044609 at 120iterations 1.4116823E-02 0.2548127 at 130iterations 8.0744075E-03 0.1417820 at 140iterations 4.6300618E-03 8.3158493E-02 at 150iterations 2.6494779E-03 4.7465801E-02 at 160iterations 1.5207066E-03 2.6725769E-02 at 170iterations 8.7521505E-04 1.5233994E-02 at 180iterations finished qdiffx linear iterations at : 16:11:58 total time elapsed so far: 20.26000 # loops : 180 mean,max change (kT/e) : 8.7521505E-04 1.5233994E-02 energy calculations done at 20.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.42000 DelPhi exited at 16:11:58 20.420u 0.457s 0:21.16 98.6% 0+0k 0+0io 0pf+0w