Sun Oct 9 02:18:02 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 Sun Oct 9 2011 at 02:18:02 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2023 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7205603 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): -32.47900 16.92700 ymin,ymax (A): -31.36000 17.59000 zmin,zma (A): -35.75900 9.503000 x,y,z range (A): 49.40600 48.95000 45.26200 scale (grids/A): 0.7205603 object centre (A): -7.776000 -6.885000 -13.12800 number of atom coordinates read : 2023 total number of charged atoms : 1928 net assigned charge : -5.279992 assigned positive charge : 307.3768 centred at (gu) : 88.92793 90.27995 92.20757 assigned negative charge : -312.6570 centred at (gu) : 88.92916 90.30006 92.16501 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7412 nv = 96 ne = 84 npr = 41090 no. pairs analyzed = 41090 no. exposed pairs = 2284 no. arc points = 16399 no. surface atoms = 764 nbur = 1259 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 524 mr = 4567 m= 3 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 261 time to turn everything in is 0.1700000 number of dielectric boundary points 3240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1317 ## 95 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7911 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8880783E-08 -4.8581384E-08 midg,1,midg; midg,igrid,midg -4.5181370E-08 -7.7917150E-08 1,midg,midg; igrid,midg,midg -7.3096118E-08 -5.0523404E-08 gauss-seidel spectral radius is 0.9899545 estimated iterations to convergence 81 setup time was (sec) 0.3800000 now iterating at: 02:18:02 rms-change max change #iterations 0.2230138 31.66408 at 10iterations 2.8717967E-02 3.802498 at 20iterations 3.6777959E-03 0.4903545 at 30iterations 4.6871809E-04 6.6994667E-02 at 40iterations 6.0614719E-05 8.7661743E-03 at 50iterations finished qdiffx linear iterations at : 02:18:06 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 6.0614719E-05 8.7661743E-03 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 02:18:06 3.646u 0.196s 0:04.12 92.9% 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 02:18:06 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2023 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.161681 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): -32.47900 16.92700 ymin,ymax (A): -31.36000 17.59000 zmin,zma (A): -35.75900 9.503000 x,y,z range (A): 49.40600 48.95000 45.26200 scale (grids/A): 2.161681 object centre (A): -7.776000 -6.885000 -13.12800 number of atom coordinates read : 2023 total number of charged atoms : 1928 net assigned charge : -5.279992 assigned positive charge : 307.3768 centred at (gu) : 86.78342 90.83995 96.62235 assigned negative charge : -312.6570 centred at (gu) : 86.78735 90.90005 96.49512 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16399 grid for indexing accessible points = 1.400000 m= 33139 mr = 57536 m= 7377 mr = 26621 m= 792 mr = 5565 m= 21 mr = 497 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6786 time to turn everything in is 0.3900000 number of dielectric boundary points 29703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15336 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) : 0.7205603 object centre at (A) : -7.776000 -6.885000 -13.12800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3884777E-02 -2.3476420E-02 midg,1,midg; midg,igrid,midg -4.6348087E-02 -2.5151787E-02 1,midg,midg; igrid,midg,midg -4.2289190E-02 -2.3766406E-02 gauss-seidel spectral radius is 0.9988595 estimated iterations to convergence 234 setup time was (sec) 0.6200000 now iterating at: 02:18:07 rms-change max change #iterations 4.770813 185.3568 at 10iterations 2.380964 75.75435 at 20iterations 1.192280 38.87861 at 30iterations 0.5971034 19.31088 at 40iterations 0.2994693 9.056965 at 50iterations 0.1500960 4.932520 at 60iterations 7.4867502E-02 2.258000 at 70iterations 3.7452843E-02 1.232271 at 80iterations 1.8765878E-02 0.5181828 at 90iterations 9.3850438E-03 0.2600212 at 100iterations 4.7084168E-03 0.1384089 at 110iterations 2.3484300E-03 7.3410034E-02 at 120iterations finished qdiffx linear iterations at : 02:18:14 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 2.3484300E-03 7.3410034E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 02:18:15 8.228u 0.227s 0:08.78 96.1% 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 02:18:15 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2023 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.242521 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): -32.47900 16.92700 ymin,ymax (A): -31.36000 17.59000 zmin,zma (A): -35.75900 9.503000 x,y,z range (A): 49.40600 48.95000 45.26200 scale (grids/A): 3.242521 object centre (A): -7.776000 -6.885000 -13.12800 number of atom coordinates read : 2023 total number of charged atoms : 1928 net assigned charge : -5.279992 assigned positive charge : 307.3768 centred at (gu) : 85.17514 91.25986 99.93349 assigned negative charge : -312.6570 centred at (gu) : 85.18105 91.35017 99.74270 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 181259 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16399 grid for indexing accessible points = 1.400000 m= 100776 mr = 137513 m= 44941 mr = 86440 m= 14465 mr = 39014 m= 3234 mr = 12130 m= 475 mr = 2634 m= 26 mr = 350 m= 0 mr = 17 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 22453 time to turn everything in is 1.220000 number of dielectric boundary points 67078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 15424 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) : 2.161681 object centre at (A) : -7.776000 -6.885000 -13.12800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4610266E-02 -0.3576957 midg,1,midg; midg,igrid,midg -0.7500255 -0.2515880 1,midg,midg; igrid,midg,midg -0.3424982 -0.2342843 gauss-seidel spectral radius is 0.9993027 estimated iterations to convergence 299 setup time was (sec) 1.470000 now iterating at: 02:18:16 rms-change max change #iterations 10.42512 391.3220 at 10iterations 6.099327 173.4203 at 20iterations 3.567037 70.13048 at 30iterations 2.085289 36.45893 at 40iterations 1.216159 21.03268 at 50iterations 0.7114478 12.77545 at 60iterations 0.4152792 6.936646 at 70iterations 0.2423573 4.447706 at 80iterations 0.1411511 2.370171 at 90iterations 8.2672879E-02 1.360386 at 100iterations 4.8123349E-02 0.8552818 at 110iterations 2.8122393E-02 0.5158653 at 120iterations 1.6420105E-02 0.3096390 at 130iterations 9.5992303E-03 0.1550541 at 140iterations 5.5886339E-03 9.7850800E-02 at 150iterations 3.2782725E-03 5.5271149E-02 at 160iterations 1.9125133E-03 3.0738831E-02 at 170iterations 1.1143795E-03 1.8290997E-02 at 180iterations finished qdiffx linear iterations at : 02:18:28 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 1.1143795E-03 1.8290997E-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 02:18:29 13.403u 0.226s 0:13.89 98.0% 0+0k 0+0io 0pf+0w