Sat Oct 8 11:38:17 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 11:38:17 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3201 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: 0.5932345 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): -17.80000 36.63600 ymin,ymax (A): -21.70800 24.79500 zmin,zma (A): -66.59700 -6.587000 x,y,z range (A): 54.43600 46.50300 60.01000 scale (grids/A): 0.5932345 object centre (A): 9.418000 1.543500 -36.59200 number of atom coordinates read : 3201 total number of charged atoms : 3040 net assigned charge : -5.999963 assigned positive charge : 467.1535 centred at (gu) : 92.36087 88.26216 89.17632 assigned negative charge : -473.1548 centred at (gu) : 92.15775 88.24151 89.14545 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7437 nv = 96 ne = 84 npr = 66796 no. pairs analyzed = 66796 no. exposed pairs = 3899 no. arc points = 26272 no. surface atoms = 1354 nbur = 1847 mkacc time = 0.1600000 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 = 1.456000 m= 348 mr = 4140 m= 0 mr = 24 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2561 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9312 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9770671E-09 -9.2328239E-10 midg,1,midg; midg,igrid,midg -4.3553152E-09 -1.0048539E-09 1,midg,midg; igrid,midg,midg -5.6064771E-09 8.6199679E-09 gauss-seidel spectral radius is 0.9853434 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 11:38:18 rms-change max change #iterations 0.1127305 18.39766 at 10iterations 1.0177227E-02 1.400377 at 20iterations 1.5890826E-03 0.2758369 at 30iterations 4.8803136E-04 7.9925537E-02 at 40iterations 1.7569559E-04 2.6206970E-02 at 50iterations finished qdiffx linear iterations at : 11:38:21 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.7569559E-04 2.6206970E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 11:38:21 3.410u 0.155s 0:04.05 87.9% 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 11:38:21 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3201 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: 1.779703 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): -17.80000 36.63600 ymin,ymax (A): -21.70800 24.79500 zmin,zma (A): -66.59700 -6.587000 x,y,z range (A): 54.43600 46.50300 60.01000 scale (grids/A): 1.779703 object centre (A): 9.418000 1.543500 -36.59200 number of atom coordinates read : 3201 total number of charged atoms : 3040 net assigned charge : -5.999963 assigned positive charge : 467.1535 centred at (gu) : 97.08139 84.78517 87.52827 assigned negative charge : -473.1548 centred at (gu) : 96.47269 84.72410 87.43597 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26272 grid for indexing accessible points = 1.400000 m= 28294 mr = 57822 m= 3869 mr = 20340 m= 173 mr = 2200 m= 0 mr = 18 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 544 time to turn everything in is 0.6000000 number of dielectric boundary points 33591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 23721 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) : 0.5932345 object centre at (A) : 9.418000 1.543500 -36.59200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9153593E-03 2.2759290E-04 midg,1,midg; midg,igrid,midg -2.1904146E-02 -7.7138422E-03 1,midg,midg; igrid,midg,midg -2.0973627E-02 1.7503303E-02 gauss-seidel spectral radius is 0.9984953 estimated iterations to convergence 204 setup time was (sec) 0.8900000 now iterating at: 11:38:22 rms-change max change #iterations 4.128963 163.6283 at 10iterations 1.860348 61.23929 at 20iterations 0.8395501 25.03414 at 30iterations 0.3807788 11.99717 at 40iterations 0.1718844 5.140683 at 50iterations 7.8053981E-02 2.336430 at 60iterations 3.5371367E-02 1.141262 at 70iterations 1.6137909E-02 0.5133858 at 80iterations 7.4995621E-03 0.2583237 at 90iterations 3.5858201E-03 0.1133041 at 100iterations 1.8043465E-03 5.9898376E-02 at 110iterations 1.0045457E-03 3.4284592E-02 at 120iterations finished qdiffx linear iterations at : 11:38:29 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 1.0045457E-03 3.4284592E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 11:38:30 7.657u 0.157s 0:08.77 88.9% 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 11:38:30 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3201 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: 2.669555 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): -17.80000 36.63600 ymin,ymax (A): -21.70800 24.79500 zmin,zma (A): -66.59700 -6.587000 x,y,z range (A): 54.43600 46.50300 60.01000 scale (grids/A): 2.669555 object centre (A): 9.418000 1.543500 -36.59200 number of atom coordinates read : 3201 total number of charged atoms : 3040 net assigned charge : -5.999963 assigned positive charge : 467.1535 centred at (gu) : 100.6220 82.17775 86.29211 assigned negative charge : -473.1548 centred at (gu) : 99.70882 82.08605 86.15385 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 189639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26272 grid for indexing accessible points = 1.400000 m= 94184 mr = 140923 m= 31125 mr = 76343 m= 6643 mr = 24188 m= 697 mr = 4685 m= 25 mr = 336 m= 0 mr = 2 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 2022 time to turn everything in is 1.510000 number of dielectric boundary points 75836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 24310 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) : 1.779703 object centre at (A) : 9.418000 1.543500 -36.59200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1562834 -1.5196786E-02 midg,1,midg; midg,igrid,midg -0.2597546 -0.1089608 1,midg,midg; igrid,midg,midg -0.2692712 0.1430312 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 1.810000 now iterating at: 11:38:34 rms-change max change #iterations 10.12002 279.5779 at 10iterations 5.926467 150.6855 at 20iterations 3.436149 71.96645 at 30iterations 1.984467 39.75723 at 40iterations 1.139732 21.82267 at 50iterations 0.6542388 12.87518 at 60iterations 0.3740934 6.926458 at 70iterations 0.2142617 3.748959 at 80iterations 0.1221229 2.202469 at 90iterations 6.9933437E-02 1.276087 at 100iterations 3.9974276E-02 0.7028122 at 110iterations 2.2851648E-02 0.4693365 at 120iterations 1.3119170E-02 0.2320290 at 130iterations 7.5859060E-03 0.1346779 at 140iterations 4.4412822E-03 8.1031799E-02 at 150iterations 2.6692725E-03 5.0136566E-02 at 160iterations 1.6751877E-03 3.2131195E-02 at 170iterations 1.1138658E-03 1.9800186E-02 at 180iterations finished qdiffx linear iterations at : 11:38:55 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 1.1138658E-03 1.9800186E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 11:38:56 12.454u 0.192s 0:25.92 48.7% 0+0k 0+0io 0pf+0w