Sat Oct 8 11:45:19 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 Sat Oct 8 2011 at 11:45:19 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 471 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5337332 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): 11.78800 76.61900 ymin,ymax (A): -26.77300 39.41200 zmin,zma (A): 76.36800 143.0680 x,y,z range (A): 64.83099 66.18500 66.69999 scale (grids/A): 0.5337332 object centre (A): 44.20350 6.319502 109.7180 number of atom coordinates read : 5441 total number of charged atoms : 5267 net assigned charge : 0.9480299 assigned positive charge : 830.7143 centred at (gu) : 89.78710 89.69527 90.73724 assigned negative charge : -829.7723 centred at (gu) : 89.82299 89.69776 90.75809 start vw surface at 0.2700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 9571 nv = 96 ne = 84 npr = 113477 no. pairs analyzed = 113477 no. exposed pairs = 6392 no. arc points = 43604 no. surface atoms = 2140 nbur = 3301 mkacc time = 0.3300000 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 = 1.596000 m= 368 mr = 5225 m= 0 mr = 13 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 4701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4356 ## 606 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 12935 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6432347E-10 -1.5255437E-10 midg,1,midg; midg,igrid,midg 6.0418621E-11 1.6044168E-11 1,midg,midg; igrid,midg,midg 3.3157185E-10 -2.3030927E-10 gauss-seidel spectral radius is 0.9820797 estimated iterations to convergence 62 setup time was (sec) 0.9500000 now iterating at: 11:45:20 rms-change max change #iterations 9.1827191E-02 11.99568 at 10iterations 7.3446510E-03 1.386971 at 20iterations 1.2846430E-03 0.3183136 at 30iterations 3.2739781E-04 7.7392578E-02 at 40iterations 8.8886685E-05 1.9424438E-02 at 50iterations finished qdiffx linear iterations at : 11:45:23 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 8.8886685E-05 1.9424438E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 11:45:24 4.316u 0.144s 0:04.98 89.3% 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 Sat Oct 8 2011 at 11:45:24 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 471 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.601200 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): 11.78800 76.61900 ymin,ymax (A): -26.77300 39.41200 zmin,zma (A): 76.36800 143.0680 x,y,z range (A): 64.83099 66.18500 66.69999 scale (grids/A): 1.601200 object centre (A): 44.20350 6.319502 109.7180 number of atom coordinates read : 5441 total number of charged atoms : 5267 net assigned charge : 0.9480299 assigned positive charge : 830.7143 centred at (gu) : 89.35943 89.08419 92.21037 assigned negative charge : -829.7723 centred at (gu) : 89.46850 89.09295 92.27384 start vw surface at 0.2700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 108582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43604 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32880 mr = 76926 m= 3268 mr = 22509 m= 82 mr = 1561 m= 0 mr = 3 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1039 time to turn everything in is 0.9500000 number of dielectric boundary points 43813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 524 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 40152 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) : 0.5337332 object centre at (A) : 44.20350 6.319502 109.7180 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2187600E-02 8.8077327E-03 midg,1,midg; midg,igrid,midg 1.3736877E-02 -2.3025100E-03 1,midg,midg; igrid,midg,midg 1.5937892E-03 -7.8450376E-03 gauss-seidel spectral radius is 0.9983402 estimated iterations to convergence 195 setup time was (sec) 1.300000 now iterating at: 11:45:26 rms-change max change #iterations 4.546409 166.1293 at 10iterations 1.970948 69.65300 at 20iterations 0.8536499 23.78070 at 30iterations 0.3716039 10.37112 at 40iterations 0.1617084 5.022976 at 50iterations 7.0147425E-02 2.028683 at 60iterations 3.0634696E-02 0.8600993 at 70iterations 1.3421918E-02 0.3941650 at 80iterations 5.9291734E-03 0.1968002 at 90iterations 2.6542214E-03 8.3099365E-02 at 100iterations 1.2158485E-03 4.3891907E-02 at 110iterations 5.7579932E-04 2.1751404E-02 at 120iterations finished qdiffx linear iterations at : 11:45:33 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 5.7579932E-04 2.1751404E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 11:45:34 9.337u 0.194s 0:09.80 97.1% 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 Sat Oct 8 2011 at 11:45:34 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 !!! WARNING: GLM 242 has a net charge of -0.0940 !!! WARNING: HIR 314 has a net charge of 0.5140 !!! WARNING: HIR 344 has a net charge of 0.5140 !!! WARNING: HIR 471 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.401799 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): 11.78800 76.61900 ymin,ymax (A): -26.77300 39.41200 zmin,zma (A): 76.36800 143.0680 x,y,z range (A): 64.83099 66.18500 66.69999 scale (grids/A): 2.401799 object centre (A): 44.20350 6.319502 109.7180 number of atom coordinates read : 5441 total number of charged atoms : 5267 net assigned charge : 0.9480299 assigned positive charge : 830.7143 centred at (gu) : 89.03880 88.62581 93.31522 assigned negative charge : -829.7723 centred at (gu) : 89.20269 88.63914 93.41074 start vw surface at 0.2700000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 253183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43604 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 115828 mr = 188587 m= 31844 mr = 91705 m= 4897 mr = 23751 m= 308 mr = 3151 m= 3 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 1.410000 no. cavity mid-points inaccessible to solvent = 3467 time to turn everything in is 2.350000 number of dielectric boundary points 98756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 42085 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) : 1.601200 object centre at (A) : 44.20350 6.319502 109.7180 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3222361 6.3732453E-02 midg,1,midg; midg,igrid,midg 0.1821059 -5.5578023E-02 1,midg,midg; igrid,midg,midg -6.8474971E-02 -0.1144116 gauss-seidel spectral radius is 0.9992377 estimated iterations to convergence 286 setup time was (sec) 2.710000 now iterating at: 11:45:37 rms-change max change #iterations 11.96392 294.6886 at 10iterations 7.069002 179.7234 at 20iterations 4.151665 103.8378 at 30iterations 2.431642 54.30277 at 40iterations 1.413246 25.69490 at 50iterations 0.8241024 19.00858 at 60iterations 0.4775149 10.65707 at 70iterations 0.2757407 5.173597 at 80iterations 0.1592911 3.060925 at 90iterations 9.1942884E-02 1.762898 at 100iterations 5.2966710E-02 1.007849 at 110iterations 3.0572796E-02 0.6051483 at 120iterations 1.7620070E-02 0.3521271 at 130iterations 1.0176635E-02 0.1961622 at 140iterations 5.8858204E-03 0.1214752 at 150iterations 3.4234466E-03 6.4765930E-02 at 160iterations 2.0035042E-03 4.1900635E-02 at 170iterations 1.1889448E-03 2.0805359E-02 at 180iterations finished qdiffx linear iterations at : 11:45:51 total time elapsed so far: 17.04000 # loops : 180 mean,max change (kT/e) : 1.1889448E-03 2.0805359E-02 energy calculations done at 17.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.27000 DelPhi exited at 11:45:52 17.271u 0.201s 0:17.75 98.4% 0+0k 0+0io 0pf+0w