Sat Oct 8 16:55:41 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 Sat Oct 8 2011 at 16:55:41 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 = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5608065 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): 21.05400 78.94900 ymin,ymax (A): 118.0070 181.4870 zmin,zma (A): -1.677000 52.98200 x,y,z range (A): 57.89500 63.48000 54.65900 scale (grids/A): 0.5608065 object centre (A): 50.00150 149.7470 25.65250 number of atom coordinates read : 4503 total number of charged atoms : 4368 net assigned charge : 1.500039 assigned positive charge : 692.9493 centred at (gu) : 90.76899 89.71999 88.72845 assigned negative charge : -691.4528 centred at (gu) : 90.79826 89.65099 88.82176 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9270 nv = 96 ne = 84 npr = 90252 no. pairs analyzed = 90252 no. exposed pairs = 5611 no. arc points = 38584 no. surface atoms = 1867 nbur = 2636 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 = 1.540000 m= 389 mr = 5017 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3918 ## 446 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12099 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4389972E-09 -1.1133270E-09 midg,1,midg; midg,igrid,midg -1.1598353E-09 1.2710368E-09 1,midg,midg; igrid,midg,midg 5.5295657E-10 -4.4934048E-10 gauss-seidel spectral radius is 0.9837153 estimated iterations to convergence 64 setup time was (sec) 0.5000000 now iterating at: 16:55:41 rms-change max change #iterations 0.1063722 14.96201 at 10iterations 8.4485402E-03 1.101604 at 20iterations 1.5918016E-03 0.2594376 at 30iterations 6.8381481E-04 0.1180248 at 40iterations 3.1487542E-04 5.4496765E-02 at 50iterations finished qdiffx linear iterations at : 16:55:44 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 3.1487542E-04 5.4496765E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 16:55:45 3.504u 0.158s 0:03.94 92.6% 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 Sat Oct 8 2011 at 16:55:45 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 = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.682420 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): 21.05400 78.94900 ymin,ymax (A): 118.0070 181.4870 zmin,zma (A): -1.677000 52.98200 x,y,z range (A): 57.89500 63.48000 54.65900 scale (grids/A): 1.682420 object centre (A): 50.00150 149.7470 25.65250 number of atom coordinates read : 4503 total number of charged atoms : 4368 net assigned charge : 1.500039 assigned positive charge : 692.9493 centred at (gu) : 92.30577 89.15878 86.18425 assigned negative charge : -691.4528 centred at (gu) : 92.39442 88.95262 86.46488 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 103453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38584 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33957 mr = 72767 m= 4143 mr = 23524 m= 149 mr = 2182 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 768 time to turn everything in is 0.5000000 number of dielectric boundary points 43202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 418 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 33723 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) : 0.5608065 object centre at (A) : 50.00150 149.7470 25.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9699941E-03 -5.3880611E-03 midg,1,midg; midg,igrid,midg 1.8475605E-02 4.8544373E-02 1,midg,midg; igrid,midg,midg -1.8435901E-02 -2.1187607E-02 gauss-seidel spectral radius is 0.9984491 estimated iterations to convergence 201 setup time was (sec) 0.7200000 now iterating at: 16:55:45 rms-change max change #iterations 4.570975 181.3902 at 10iterations 2.026167 64.06751 at 20iterations 0.9063635 26.56879 at 30iterations 0.4015445 11.79668 at 40iterations 0.1800661 5.554541 at 50iterations 8.0450922E-02 2.702917 at 60iterations 3.6077674E-02 1.136422 at 70iterations 1.6197708E-02 0.4546233 at 80iterations 7.4527734E-03 0.2150574 at 90iterations 3.5907181E-03 0.1110535 at 100iterations 1.8918891E-03 6.2614441E-02 at 110iterations 1.1233363E-03 4.1959763E-02 at 120iterations finished qdiffx linear iterations at : 16:55:53 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 1.1233363E-03 4.1959763E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 16:55:53 8.058u 0.203s 0:08.53 96.7% 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 Sat Oct 8 2011 at 16:55:53 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 = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.523629 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): 21.05400 78.94900 ymin,ymax (A): 118.0070 181.4870 zmin,zma (A): -1.677000 52.98200 x,y,z range (A): 57.89500 63.48000 54.65900 scale (grids/A): 2.523629 object centre (A): 50.00150 149.7470 25.65250 number of atom coordinates read : 4503 total number of charged atoms : 4368 net assigned charge : 1.500039 assigned positive charge : 692.9493 centred at (gu) : 93.45837 88.73763 84.27615 assigned negative charge : -691.4528 centred at (gu) : 93.59168 88.42888 84.69728 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 240340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38584 grid for indexing accessible points = 1.400000 m= 115973 mr = 177713 m= 35379 mr = 92388 m= 6867 mr = 26673 m= 673 mr = 4683 m= 14 mr = 344 m= 0 mr = 2 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 2732 time to turn everything in is 1.220000 number of dielectric boundary points 97443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 34920 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) : 1.682420 object centre at (A) : 50.00150 149.7470 25.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5261558E-02 -7.6324902E-02 midg,1,midg; midg,igrid,midg 0.3650821 0.8792073 1,midg,midg; igrid,midg,midg -0.2726318 -0.3298048 gauss-seidel spectral radius is 0.9992518 estimated iterations to convergence 289 setup time was (sec) 1.470000 now iterating at: 16:55:55 rms-change max change #iterations 11.55174 391.5461 at 10iterations 6.793734 201.7332 at 20iterations 3.976980 80.39573 at 30iterations 2.314318 48.20277 at 40iterations 1.343710 24.69070 at 50iterations 0.7781553 13.62168 at 60iterations 0.4494575 8.178122 at 70iterations 0.2591362 4.290619 at 80iterations 0.1494384 2.431946 at 90iterations 8.6009860E-02 1.430528 at 100iterations 4.9508892E-02 0.8403770 at 110iterations 2.8530823E-02 0.4667263 at 120iterations 1.6419986E-02 0.2844065 at 130iterations 9.5283519E-03 0.1553307 at 140iterations 5.5714301E-03 0.1086884 at 150iterations 3.3190199E-03 6.1731339E-02 at 160iterations 2.0460405E-03 4.1217804E-02 at 170iterations 1.3224031E-03 2.7664185E-02 at 180iterations finished qdiffx linear iterations at : 16:56:07 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 1.3224031E-03 2.7664185E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 16:56:07 13.402u 0.216s 0:13.90 97.9% 0+0k 0+0io 0pf+0w