Sat Oct 8 16:43:15 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 16:43:16 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4568 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5469519 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): 16.92800 78.89300 ymin,ymax (A): 119.1950 184.2830 zmin,zma (A): -1.737000 59.69700 x,y,z range (A): 61.96500 65.08799 61.43400 scale (grids/A): 0.5469519 object centre (A): 47.91050 151.7390 28.98000 number of atom coordinates read : 4568 total number of charged atoms : 4390 net assigned charge : 3.000042 assigned positive charge : 701.5067 centred at (gu) : 91.70544 89.26680 87.25393 assigned negative charge : -698.5102 centred at (gu) : 91.66685 89.17909 87.26694 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8727 nv = 96 ne = 84 npr = 91908 no. pairs analyzed = 91908 no. exposed pairs = 5453 no. arc points = 37918 no. surface atoms = 1842 nbur = 2726 mkacc time = 0.2000000 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 = 1.568000 m= 400 mr = 4724 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3927 ## 536 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 11673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4484867E-10 2.7506450E-11 midg,1,midg; midg,igrid,midg -9.1577534E-10 9.2797559E-10 1,midg,midg; igrid,midg,midg -1.4579481E-10 9.1475233E-10 gauss-seidel spectral radius is 0.9828822 estimated iterations to convergence 63 setup time was (sec) 0.7100000 now iterating at: 16:43:16 rms-change max change #iterations 9.3705349E-02 14.61378 at 10iterations 6.5687704E-03 0.9740906 at 20iterations 6.3837628E-04 9.0509415E-02 at 30iterations 1.5012945E-04 2.0880699E-02 at 40iterations 4.6003144E-05 6.8740845E-03 at 50iterations finished qdiffx linear iterations at : 16:43:20 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 4.6003144E-05 6.8740845E-03 energy calculations done at 4.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 16:43:20 4.328u 0.259s 0:04.88 93.6% 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 16:43:20 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4568 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.640856 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): 16.92800 78.89300 ymin,ymax (A): 119.1950 184.2830 zmin,zma (A): -1.737000 59.69700 x,y,z range (A): 61.96500 65.08799 61.43400 scale (grids/A): 1.640856 object centre (A): 47.91050 151.7390 28.98000 number of atom coordinates read : 4568 total number of charged atoms : 4390 net assigned charge : 3.000042 assigned positive charge : 701.5067 centred at (gu) : 95.11510 87.79880 81.76073 assigned negative charge : -698.5102 centred at (gu) : 95.00057 87.53700 81.80067 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 98371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37918 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30858 mr = 69023 m= 3484 mr = 21454 m= 110 mr = 1951 m= 0 mr = 19 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.7200000 number of dielectric boundary points 40376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 33660 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) : 0.5469519 object centre at (A) : 47.91050 151.7390 28.98000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8257567E-03 8.4459856E-03 midg,1,midg; midg,igrid,midg 1.4695994E-02 3.3852544E-02 1,midg,midg; igrid,midg,midg -1.0689267E-02 -1.5234036E-02 gauss-seidel spectral radius is 0.9983528 estimated iterations to convergence 196 setup time was (sec) 1.060000 now iterating at: 16:43:22 rms-change max change #iterations 4.370999 203.9157 at 10iterations 1.896891 92.69912 at 20iterations 0.8216776 30.97477 at 30iterations 0.3579495 11.68584 at 40iterations 0.1560430 5.161548 at 50iterations 6.7887686E-02 2.161375 at 60iterations 2.9530074E-02 0.9568939 at 70iterations 1.2884828E-02 0.3697433 at 80iterations 5.6359558E-03 0.1783829 at 90iterations 2.4685368E-03 7.5111389E-02 at 100iterations 1.0937547E-03 3.2989502E-02 at 110iterations 4.8718150E-04 1.4936447E-02 at 120iterations finished qdiffx linear iterations at : 16:43:30 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 4.8718150E-04 1.4936447E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.930000 DelPhi exited at 16:43:31 9.930u 0.251s 0:10.47 97.2% 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 16:43:31 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4568 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.461284 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): 16.92800 78.89300 ymin,ymax (A): 119.1950 184.2830 zmin,zma (A): -1.737000 59.69700 x,y,z range (A): 61.96500 65.08799 61.43400 scale (grids/A): 2.461284 object centre (A): 47.91050 151.7390 28.98000 number of atom coordinates read : 4568 total number of charged atoms : 4390 net assigned charge : 3.000042 assigned positive charge : 701.5067 centred at (gu) : 97.67255 86.69819 77.64078 assigned negative charge : -698.5102 centred at (gu) : 97.50067 86.30559 77.70082 start vw surface at 0.1900000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 229248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37918 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106599 mr = 168864 m= 31249 mr = 85319 m= 5808 mr = 23756 m= 507 mr = 4125 m= 6 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 803 time to turn everything in is 1.770000 number of dielectric boundary points 91067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 35085 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) : 1.640856 object centre at (A) : 47.91050 151.7390 28.98000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7183077E-03 0.1785317 midg,1,midg; midg,igrid,midg 0.2211426 0.6060456 1,midg,midg; igrid,midg,midg -0.1422794 -0.2528282 gauss-seidel spectral radius is 0.9992180 estimated iterations to convergence 282 setup time was (sec) 2.140000 now iterating at: 16:43:33 rms-change max change #iterations 11.16475 340.5575 at 10iterations 6.455618 133.7941 at 20iterations 3.703488 70.66100 at 30iterations 2.124558 40.69214 at 40iterations 1.211872 25.62928 at 50iterations 0.6908681 12.07020 at 60iterations 0.3928703 6.774483 at 70iterations 0.2228556 4.121475 at 80iterations 0.1266422 2.063213 at 90iterations 7.1709596E-02 1.125633 at 100iterations 4.0597163E-02 0.6634722 at 110iterations 2.3044821E-02 0.4375858 at 120iterations 1.3050272E-02 0.2545624 at 130iterations 7.3835705E-03 0.1242510 at 140iterations 4.1819396E-03 6.7001343E-02 at 150iterations 2.3691661E-03 3.9644718E-02 at 160iterations 1.3389935E-03 2.2430420E-02 at 170iterations 7.5881887E-04 1.3439178E-02 at 180iterations finished qdiffx linear iterations at : 16:43:47 total time elapsed so far: 16.07000 # loops : 180 mean,max change (kT/e) : 7.5881887E-04 1.3439178E-02 energy calculations done at 16.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.25000 DelPhi exited at 16:43:48 16.254u 0.265s 0:16.80 98.2% 0+0k 0+0io 0pf+0w