Sat Oct 8 11:36:40 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 11:36:40 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3936 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5121713 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): -1.976000 67.53200 ymin,ymax (A): -9.862000 38.79400 zmin,zma (A): -19.63300 41.04800 x,y,z range (A): 69.50800 48.65600 60.68100 scale (grids/A): 0.5121713 object centre (A): 32.77800 14.46600 10.70750 number of atom coordinates read : 3936 total number of charged atoms : 3783 net assigned charge : -7.999949 assigned positive charge : 589.2106 centred at (gu) : 88.19292 89.94963 91.16306 assigned negative charge : -597.2124 centred at (gu) : 88.20724 90.03671 91.23380 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6462 nv = 96 ne = 84 npr = 82381 no. pairs analyzed = 82381 no. exposed pairs = 4566 no. arc points = 30805 no. surface atoms = 1558 nbur = 2378 mkacc time = 0.2100000 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 = 1.652000 m= 216 mr = 3530 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.4100000 number of dielectric boundary points 3142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3103 ## 440 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8710 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9667342E-11 -3.8633535E-10 midg,1,midg; midg,igrid,midg 8.0016056E-11 -3.1848199E-10 1,midg,midg; igrid,midg,midg -1.3687707E-10 -9.6323560E-11 gauss-seidel spectral radius is 0.9804360 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 11:36:41 rms-change max change #iterations 6.1951715E-02 10.90402 at 10iterations 3.8640571E-03 0.7129364 at 20iterations 5.2322011E-04 7.9048157E-02 at 30iterations 1.4321835E-04 2.4507523E-02 at 40iterations 4.3801403E-05 7.7686310E-03 at 50iterations finished qdiffx linear iterations at : 11:36:45 total time elapsed so far: 4.580000 # loops : 50 mean,max change (kT/e) : 4.3801403E-05 7.7686310E-03 energy calculations done at 4.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.740000 DelPhi exited at 11:36:46 4.744u 0.368s 0:05.64 90.4% 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 11:36:46 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3936 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.536514 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): -1.976000 67.53200 ymin,ymax (A): -9.862000 38.79400 zmin,zma (A): -19.63300 41.04800 x,y,z range (A): 69.50800 48.65600 60.68100 scale (grids/A): 1.536514 object centre (A): 32.77800 14.46600 10.70750 number of atom coordinates read : 3936 total number of charged atoms : 3783 net assigned charge : -7.999949 assigned positive charge : 589.2106 centred at (gu) : 84.57758 89.84784 93.48840 assigned negative charge : -597.2124 centred at (gu) : 84.62118 90.10969 93.70102 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30805 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 21705 mr = 52636 m= 1927 mr = 14802 m= 34 mr = 859 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1577 time to turn everything in is 0.6000000 number of dielectric boundary points 29255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 412 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 28501 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) : 0.5121713 object centre at (A) : 32.77800 14.46600 10.70750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4996313E-03 -1.6197661E-02 midg,1,midg; midg,igrid,midg -1.6233461E-03 -8.5248519E-03 1,midg,midg; igrid,midg,midg 9.8093702E-03 -4.1251634E-03 gauss-seidel spectral radius is 0.9980230 estimated iterations to convergence 179 setup time was (sec) 0.8900000 now iterating at: 11:36:47 rms-change max change #iterations 3.424002 151.4751 at 10iterations 1.374130 53.69247 at 20iterations 0.5524601 19.63346 at 30iterations 0.2215952 9.062941 at 40iterations 8.9485846E-02 3.946308 at 50iterations 3.6217581E-02 1.270828 at 60iterations 1.4653901E-02 0.5408573 at 70iterations 5.9760627E-03 0.2021008 at 80iterations 2.5027532E-03 9.3246460E-02 at 90iterations 1.0966862E-03 4.1534424E-02 at 100iterations 5.3033000E-04 1.9422531E-02 at 110iterations 2.8640334E-04 1.0413170E-02 at 120iterations finished qdiffx linear iterations at : 11:36:57 total time elapsed so far: 10.59000 # loops : 120 mean,max change (kT/e) : 2.8640334E-04 1.0413170E-02 energy calculations done at 10.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.76000 DelPhi exited at 11:36:58 10.762u 0.442s 0:11.57 96.8% 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 11:36:58 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3936 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.304771 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): -1.976000 67.53200 ymin,ymax (A): -9.862000 38.79400 zmin,zma (A): -19.63300 41.04800 x,y,z range (A): 69.50800 48.65600 60.68100 scale (grids/A): 2.304771 object centre (A): 32.77800 14.46600 10.70750 number of atom coordinates read : 3936 total number of charged atoms : 3783 net assigned charge : -7.999949 assigned positive charge : 589.2106 centred at (gu) : 81.86595 89.77135 95.23244 assigned negative charge : -597.2124 centred at (gu) : 81.93173 90.16435 95.55142 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 172315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30805 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 77956 mr = 128594 m= 19943 mr = 62121 m= 2804 mr = 14621 m= 123 mr = 1748 m= 0 mr = 24 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 5307 time to turn everything in is 1.470000 number of dielectric boundary points 66033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 30196 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) : 1.536514 object centre at (A) : 32.77800 14.46600 10.70750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1160853 -0.2931435 midg,1,midg; midg,igrid,midg -4.4260141E-02 -0.1363495 1,midg,midg; igrid,midg,midg 0.4652738 -0.2693907 gauss-seidel spectral radius is 0.9991022 estimated iterations to convergence 264 setup time was (sec) 1.860000 now iterating at: 11:37:00 rms-change max change #iterations 9.151811 246.2519 at 10iterations 5.085028 148.2159 at 20iterations 2.809941 65.08950 at 30iterations 1.544200 31.46606 at 40iterations 0.8464913 17.15536 at 50iterations 0.4632796 9.945595 at 60iterations 0.2530641 5.768324 at 70iterations 0.1382136 2.832399 at 80iterations 7.5402737E-02 1.577688 at 90iterations 4.1101146E-02 0.9624691 at 100iterations 2.2371015E-02 0.4702682 at 110iterations 1.2202440E-02 0.2310810 at 120iterations 6.6785975E-03 0.1387863 at 130iterations 3.6743460E-03 7.4645996E-02 at 140iterations 2.0433927E-03 4.3708891E-02 at 150iterations 1.1605688E-03 2.4335861E-02 at 160iterations 6.7889708E-04 1.3742447E-02 at 170iterations 4.1731098E-04 9.0904236E-03 at 180iterations finished qdiffx linear iterations at : 11:37:17 total time elapsed so far: 19.09000 # loops : 180 mean,max change (kT/e) : 4.1731098E-04 9.0904236E-03 energy calculations done at 19.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.26000 DelPhi exited at 11:37:18 19.264u 0.458s 0:20.04 98.3% 0+0k 0+0io 0pf+0w