Sun Oct 9 11:54:48 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 Sun Oct 9 2011 at 11:54:48 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2648 !!! WARNING: HIQ 202 has a net charge of 0.5140 !!! WARNING: VAL 224 has a net charge of -0.2720 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: 0.6633375 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): 51.41600 104.0460 ymin,ymax (A): 5.389000 58.17500 zmin,zma (A): 34.44000 88.10800 x,y,z range (A): 52.63000 52.78600 53.66800 scale (grids/A): 0.6633375 object centre (A): 77.73100 31.78200 61.27400 number of atom coordinates read : 2648 total number of charged atoms : 2576 net assigned charge : 0.2420081 assigned positive charge : 391.5572 centred at (gu) : 89.32735 89.47454 92.78625 assigned negative charge : -391.3167 centred at (gu) : 89.50809 89.55605 92.72025 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8573 nv = 96 ne = 84 npr = 50110 no. pairs analyzed = 50110 no. exposed pairs = 3761 no. arc points = 26921 no. surface atoms = 1261 nbur = 1387 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 589 mr = 4432 m= 3 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3100000 number of dielectric boundary points 4638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9701 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0790175E-09 2.5429513E-08 midg,1,midg; midg,igrid,midg 1.9306142E-08 -1.5957369E-08 1,midg,midg; igrid,midg,midg 4.3892420E-08 -3.4539436E-08 gauss-seidel spectral radius is 0.9882511 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 11:54:49 rms-change max change #iterations 0.1737159 24.45655 at 10iterations 1.8790448E-02 2.619307 at 20iterations 2.1732720E-03 0.2794113 at 30iterations 3.7648404E-04 6.3743591E-02 at 40iterations 1.0956825E-04 2.0561218E-02 at 50iterations finished qdiffx linear iterations at : 11:54:51 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.0956825E-04 2.0561218E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 11:54:52 3.429u 0.167s 0:03.87 92.5% 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 Sun Oct 9 2011 at 11:54:52 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2648 !!! WARNING: HIQ 202 has a net charge of 0.5140 !!! WARNING: VAL 224 has a net charge of -0.2720 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: 1.990013 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): 51.41600 104.0460 ymin,ymax (A): 5.389000 58.17500 zmin,zma (A): 34.44000 88.10800 x,y,z range (A): 52.63000 52.78600 53.66800 scale (grids/A): 1.990013 object centre (A): 77.73100 31.78200 61.27400 number of atom coordinates read : 2648 total number of charged atoms : 2576 net assigned charge : 0.2420081 assigned positive charge : 391.5572 centred at (gu) : 87.98126 88.42287 98.35825 assigned negative charge : -391.3167 centred at (gu) : 88.52419 88.66784 98.16068 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26921 grid for indexing accessible points = 1.400000 m= 35313 mr = 60207 m= 7546 mr = 25594 m= 638 mr = 4941 m= 10 mr = 300 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 42709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20387 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) : 0.6633375 object centre at (A) : 77.73100 31.78200 61.27400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3296475E-02 7.1566693E-02 midg,1,midg; midg,igrid,midg 2.1654546E-02 5.8453986E-03 1,midg,midg; igrid,midg,midg 3.0198758E-02 -4.4597037E-02 gauss-seidel spectral radius is 0.9987845 estimated iterations to convergence 227 setup time was (sec) 0.9800000 now iterating at: 11:54:53 rms-change max change #iterations 4.726676 189.5468 at 10iterations 2.317300 66.45290 at 20iterations 1.129531 33.34791 at 30iterations 0.5523468 16.72136 at 40iterations 0.2706947 8.344948 at 50iterations 0.1324638 4.206268 at 60iterations 6.4592279E-02 2.227516 at 70iterations 3.1690650E-02 1.039265 at 80iterations 1.5514898E-02 0.4860253 at 90iterations 7.6111546E-03 0.2211475 at 100iterations 3.7528062E-03 0.1098432 at 110iterations 1.8532848E-03 5.5836111E-02 at 120iterations finished qdiffx linear iterations at : 11:55:00 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.8532848E-03 5.5836111E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 11:55:00 7.799u 0.183s 0:08.25 96.6% 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 Sun Oct 9 2011 at 11:55:00 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2648 !!! WARNING: HIQ 202 has a net charge of 0.5140 !!! WARNING: VAL 224 has a net charge of -0.2720 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: 2.985019 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): 51.41600 104.0460 ymin,ymax (A): 5.389000 58.17500 zmin,zma (A): 34.44000 88.10800 x,y,z range (A): 52.63000 52.78600 53.66800 scale (grids/A): 2.985019 object centre (A): 77.73100 31.78200 61.27400 number of atom coordinates read : 2648 total number of charged atoms : 2576 net assigned charge : 0.2420081 assigned positive charge : 391.5572 centred at (gu) : 86.97177 87.63396 102.5373 assigned negative charge : -391.3167 centred at (gu) : 87.78622 88.00188 102.2409 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 207925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26921 grid for indexing accessible points = 1.400000 m= 108066 mr = 146316 m= 45918 mr = 86586 m= 14269 mr = 36728 m= 2716 mr = 11025 m= 230 mr = 1949 m= 1 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.790000 number of dielectric boundary points 96417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 20607 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) : 1.990013 object centre at (A) : 77.73100 31.78200 61.27400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1221798 0.9077203 midg,1,midg; midg,igrid,midg 0.2148556 -0.1270975 1,midg,midg; igrid,midg,midg 0.2084908 -0.4110814 gauss-seidel spectral radius is 0.9993271 estimated iterations to convergence 304 setup time was (sec) 2.090000 now iterating at: 11:55:02 rms-change max change #iterations 11.06781 370.5358 at 10iterations 6.715340 133.9165 at 20iterations 4.042485 99.19411 at 30iterations 2.423679 47.31342 at 40iterations 1.450647 29.21097 at 50iterations 0.8643499 15.25970 at 60iterations 0.5148146 9.545231 at 70iterations 0.3059474 5.267006 at 80iterations 0.1815560 3.173384 at 90iterations 0.1074844 1.867542 at 100iterations 6.3767083E-02 1.131672 at 110iterations 3.7728615E-02 0.6477356 at 120iterations 2.2315858E-02 0.3553619 at 130iterations 1.3207024E-02 0.2207382 at 140iterations 7.8113135E-03 0.1315002 at 150iterations 4.6629282E-03 8.5321426E-02 at 160iterations 2.7820379E-03 4.6234131E-02 at 170iterations 1.6849145E-03 3.2432556E-02 at 180iterations finished qdiffx linear iterations at : 11:55:13 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 1.6849145E-03 3.2432556E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 11:55:14 13.026u 0.210s 0:13.51 97.9% 0+0k 0+0io 0pf+0w