Sun Oct 9 07:15:10 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 07:15:10 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 = 2497 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: 0.5469854 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): -5.020000 41.34400 ymin,ymax (A): 37.25500 89.41100 zmin,zma (A): -3.171000 61.91300 x,y,z range (A): 46.36400 52.15599 65.08400 scale (grids/A): 0.5469854 object centre (A): 18.16200 63.33300 29.37100 number of atom coordinates read : 2497 total number of charged atoms : 2351 net assigned charge : -9.499980 assigned positive charge : 373.8769 centred at (gu) : 90.92893 88.31876 89.41260 assigned negative charge : -383.3773 centred at (gu) : 91.10288 87.92955 89.34935 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 4846 nv = 96 ne = 84 npr = 50056 no. pairs analyzed = 50056 no. exposed pairs = 3511 no. arc points = 24810 no. surface atoms = 1183 nbur = 1314 mkacc time = 0.1100000 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= 185 mr = 2253 m= 0 mr = 7 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2446 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0692142E-09 -1.5806105E-10 midg,1,midg; midg,igrid,midg -4.5298254E-09 1.0733341E-09 1,midg,midg; igrid,midg,midg 3.5627931E-10 -2.0152413E-09 gauss-seidel spectral radius is 0.9827359 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 07:15:11 rms-change max change #iterations 6.5796517E-02 15.09406 at 10iterations 4.2134840E-03 0.6965027 at 20iterations 2.9005442E-04 6.5147400E-02 at 30iterations 1.8651572E-05 3.8299561E-03 at 40iterations 1.2907142E-06 3.0088425E-04 at 50iterations finished qdiffx linear iterations at : 07:15:13 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.2907142E-06 3.0088425E-04 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:15:14 3.326u 0.209s 0:03.81 92.3% 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 07:15:14 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 = 2497 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: 1.640956 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): -5.020000 41.34400 ymin,ymax (A): 37.25500 89.41100 zmin,zma (A): -3.171000 61.91300 x,y,z range (A): 46.36400 52.15599 65.08400 scale (grids/A): 1.640956 object centre (A): 18.16200 63.33300 29.37100 number of atom coordinates read : 2497 total number of charged atoms : 2351 net assigned charge : -9.499980 assigned positive charge : 373.8769 centred at (gu) : 92.78620 84.95571 88.23698 assigned negative charge : -383.3773 centred at (gu) : 93.30843 83.78847 88.04764 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 53139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24810 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14881 mr = 33472 m= 1358 mr = 9420 m= 28 mr = 564 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.4100000 number of dielectric boundary points 25950 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 258 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17990 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) : 0.5469854 object centre at (A) : 18.16200 63.33300 29.37100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2453991E-02 8.4017683E-03 midg,1,midg; midg,igrid,midg -3.1233301E-02 5.0296346E-03 1,midg,midg; igrid,midg,midg -3.6703756E-03 -1.5265131E-02 gauss-seidel spectral radius is 0.9981477 estimated iterations to convergence 185 setup time was (sec) 0.6900000 now iterating at: 07:15:15 rms-change max change #iterations 3.022457 157.0110 at 10iterations 1.247583 52.76359 at 20iterations 0.5120333 25.10456 at 30iterations 0.2105272 8.723892 at 40iterations 8.7232433E-02 4.155178 at 50iterations 3.5913598E-02 1.663285 at 60iterations 1.4864230E-02 0.5747678 at 70iterations 6.0966574E-03 0.2528293 at 80iterations 2.5180401E-03 0.1104088 at 90iterations 1.0371669E-03 4.0615037E-02 at 100iterations 4.2896764E-04 1.8047810E-02 at 110iterations 1.7688928E-04 7.2784424E-03 at 120iterations finished qdiffx linear iterations at : 07:15:21 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 1.7688928E-04 7.2784424E-03 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 07:15:22 7.307u 0.219s 0:07.82 96.0% 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 07:15:22 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 = 2497 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: 2.461434 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): -5.020000 41.34400 ymin,ymax (A): 37.25500 89.41100 zmin,zma (A): -3.171000 61.91300 x,y,z range (A): 46.36400 52.15599 65.08400 scale (grids/A): 2.461434 object centre (A): 18.16200 63.33300 29.37100 number of atom coordinates read : 2497 total number of charged atoms : 2351 net assigned charge : -9.499980 assigned positive charge : 373.8769 centred at (gu) : 94.17918 82.43343 87.35536 assigned negative charge : -383.3773 centred at (gu) : 94.96262 80.68263 87.07132 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 123351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24810 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 51970 mr = 82375 m= 13395 mr = 39163 m= 1984 mr = 9493 m= 128 mr = 1196 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.9400000 number of dielectric boundary points 58556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 18786 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) : 1.640956 object centre at (A) : 18.16200 63.33300 29.37100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8484293 8.4888533E-02 midg,1,midg; midg,igrid,midg -0.4434807 8.0763258E-02 1,midg,midg; igrid,midg,midg -5.4894090E-02 -0.1942008 gauss-seidel spectral radius is 0.9991155 estimated iterations to convergence 266 setup time was (sec) 1.260000 now iterating at: 07:15:23 rms-change max change #iterations 8.017240 307.7859 at 10iterations 4.441014 129.0091 at 20iterations 2.458640 73.04278 at 30iterations 1.356832 37.79015 at 40iterations 0.7469390 17.56088 at 50iterations 0.4093503 10.40297 at 60iterations 0.2242620 5.516741 at 70iterations 0.1227899 2.759346 at 80iterations 6.6927992E-02 1.486632 at 90iterations 3.6574561E-02 0.9053116 at 100iterations 2.0005606E-02 0.5076933 at 110iterations 1.0873339E-02 0.2610331 at 120iterations 5.9236214E-03 0.1469116 at 130iterations 3.2268302E-03 8.2286507E-02 at 140iterations 1.7585952E-03 3.8627625E-02 at 150iterations 9.5583737E-04 2.1827698E-02 at 160iterations 5.2268512E-04 1.2683868E-02 at 170iterations 2.8417530E-04 6.4039230E-03 at 180iterations finished qdiffx linear iterations at : 07:15:33 total time elapsed so far: 11.52000 # loops : 180 mean,max change (kT/e) : 2.8417530E-04 6.4039230E-03 energy calculations done at 11.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 07:15:34 11.699u 0.222s 0:12.19 97.7% 0+0k 0+0io 0pf+0w