Sat Oct 8 17:48:56 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 17:48:56 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3082 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5518781 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): -39.09900 10.65400 ymin,ymax (A): 7.939000 72.44600 zmin,zma (A): 63.53800 109.8530 x,y,z range (A): 49.75300 64.50700 46.31499 scale (grids/A): 0.5518781 object centre (A): -14.22250 40.19250 86.69550 number of atom coordinates read : 3082 total number of charged atoms : 2941 net assigned charge : 0.5000044 assigned positive charge : 453.9131 centred at (gu) : 89.61755 89.11197 90.34121 assigned negative charge : -453.4142 centred at (gu) : 89.54951 89.08837 90.33774 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6260 nv = 96 ne = 84 npr = 62346 no. pairs analyzed = 62346 no. exposed pairs = 3810 no. arc points = 25954 no. surface atoms = 1294 nbur = 1788 mkacc time = 0.1100000 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 = 1.540000 m= 266 mr = 3392 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2200000 number of dielectric boundary points 3116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2733 ## 337 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8113 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3317436E-11 7.9132784E-11 midg,1,midg; midg,igrid,midg -1.9523799E-10 1.9437287E-10 1,midg,midg; igrid,midg,midg -5.8853827E-10 5.5673988E-10 gauss-seidel spectral radius is 0.9830765 estimated iterations to convergence 63 setup time was (sec) 0.4200000 now iterating at: 17:48:57 rms-change max change #iterations 7.6717176E-02 14.07431 at 10iterations 5.2665421E-03 0.7960796 at 20iterations 3.7892270E-04 6.1974525E-02 at 30iterations 3.6083195E-05 7.0667267E-03 at 40iterations 6.3491807E-06 1.5249848E-03 at 50iterations finished qdiffx linear iterations at : 17:49:00 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 6.3491807E-06 1.5249848E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 17:49:00 3.607u 0.193s 0:04.06 93.3% 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 17:49:00 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3082 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.655634 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): -39.09900 10.65400 ymin,ymax (A): 7.939000 72.44600 zmin,zma (A): 63.53800 109.8530 x,y,z range (A): 49.75300 64.50700 46.31499 scale (grids/A): 1.655634 object centre (A): -14.22250 40.19250 86.69550 number of atom coordinates read : 3082 total number of charged atoms : 2941 net assigned charge : 0.5000044 assigned positive charge : 453.9131 centred at (gu) : 88.85188 87.33514 91.02296 assigned negative charge : -453.4142 centred at (gu) : 88.64832 87.26495 91.01285 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25954 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23178 mr = 48626 m= 2643 mr = 16411 m= 73 mr = 1351 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 376 time to turn everything in is 0.3400000 number of dielectric boundary points 28788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 22584 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) : 0.5518781 object centre at (A) : -14.22250 40.19250 86.69550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3395143E-03 -3.1290438E-03 midg,1,midg; midg,igrid,midg 2.1844363E-02 -2.4474801E-02 1,midg,midg; igrid,midg,midg 3.9213463E-03 1.1131458E-02 gauss-seidel spectral radius is 0.9982458 estimated iterations to convergence 190 setup time was (sec) 0.5700000 now iterating at: 17:49:01 rms-change max change #iterations 3.422546 167.9866 at 10iterations 1.443666 56.73192 at 20iterations 0.6138332 22.56216 at 30iterations 0.2608552 9.461002 at 40iterations 0.1105523 3.893880 at 50iterations 4.6611283E-02 1.553958 at 60iterations 1.9820899E-02 0.7012119 at 70iterations 8.4186643E-03 0.3100090 at 80iterations 3.5777951E-03 0.1300735 at 90iterations 1.5199785E-03 5.0819397E-02 at 100iterations 6.5048644E-04 2.5762558E-02 at 110iterations 2.7882186E-04 9.6759796E-03 at 120iterations finished qdiffx linear iterations at : 17:49:09 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 2.7882186E-04 9.6759796E-03 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 17:49:09 8.174u 0.232s 0:08.70 96.5% 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 17:49:09 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3082 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.483452 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): -39.09900 10.65400 ymin,ymax (A): 7.939000 72.44600 zmin,zma (A): 63.53800 109.8530 x,y,z range (A): 49.75300 64.50700 46.31499 scale (grids/A): 2.483452 object centre (A): -14.22250 40.19250 86.69550 number of atom coordinates read : 3082 total number of charged atoms : 2941 net assigned charge : 0.5000044 assigned positive charge : 453.9131 centred at (gu) : 88.27753 86.00256 91.53435 assigned negative charge : -453.4142 centred at (gu) : 87.97242 85.89723 91.51920 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 160852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25954 grid for indexing accessible points = 1.400000 m= 79297 mr = 118700 m= 24074 mr = 63934 m= 4297 mr = 18249 m= 339 mr = 2893 m= 7 mr = 155 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 1220 time to turn everything in is 0.8700000 number of dielectric boundary points 64935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 23505 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) : 1.655634 object centre at (A) : -14.22250 40.19250 86.69550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5230867E-02 -3.8504768E-02 midg,1,midg; midg,igrid,midg 0.5353064 -0.3930379 1,midg,midg; igrid,midg,midg 8.8946663E-02 0.1578504 gauss-seidel spectral radius is 0.9991567 estimated iterations to convergence 272 setup time was (sec) 1.130000 now iterating at: 17:49:11 rms-change max change #iterations 8.789174 321.5295 at 10iterations 4.970855 137.2266 at 20iterations 2.793965 76.07912 at 30iterations 1.563639 35.63910 at 40iterations 0.8724157 17.35544 at 50iterations 0.4850014 11.69255 at 60iterations 0.2694546 5.202497 at 70iterations 0.1498284 2.908111 at 80iterations 8.2930535E-02 1.786469 at 90iterations 4.6076279E-02 0.9504766 at 100iterations 2.5475459E-02 0.4794159 at 110iterations 1.4170554E-02 0.2982635 at 120iterations 7.8423359E-03 0.1592908 at 130iterations 4.3426240E-03 8.7853432E-02 at 140iterations 2.4053857E-03 5.0110817E-02 at 150iterations 1.3373346E-03 2.7038574E-02 at 160iterations 7.4534724E-04 1.5033722E-02 at 170iterations 4.1837044E-04 9.1915131E-03 at 180iterations finished qdiffx linear iterations at : 17:49:23 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 4.1837044E-04 9.1915131E-03 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 17:49:23 13.228u 0.236s 0:13.75 97.8% 0+0k 0+0io 0pf+0w