Tue Oct 11 06:54:22 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 Tue Oct 11 2011 at 06:54:22 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 = 2903 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: 0.5473976 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): -19.94300 45.09200 ymin,ymax (A): 19.25400 75.99500 zmin,zma (A): -70.41300 -20.95200 x,y,z range (A): 65.03500 56.74100 49.46100 scale (grids/A): 0.5473976 object centre (A): 12.57450 47.62450 -45.68250 number of atom coordinates read : 2903 total number of charged atoms : 2763 net assigned charge : -1.499988 assigned positive charge : 421.3496 centred at (gu) : 89.89531 89.74514 89.67383 assigned negative charge : -422.8503 centred at (gu) : 89.94215 89.84045 89.70317 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5647 nv = 96 ne = 84 npr = 59386 no. pairs analyzed = 59386 no. exposed pairs = 3595 no. arc points = 25776 no. surface atoms = 1219 nbur = 1684 mkacc time = 0.1300000 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= 224 mr = 2944 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2585 ## 337 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7361 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0216682E-10 -2.7466740E-10 midg,1,midg; midg,igrid,midg 5.6216459E-10 -6.9882750E-10 1,midg,midg; igrid,midg,midg 2.1503249E-10 -4.0485348E-10 gauss-seidel spectral radius is 0.9827903 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 06:54:23 rms-change max change #iterations 7.3778898E-02 13.04146 at 10iterations 4.9199220E-03 0.8784156 at 20iterations 3.3154388E-04 5.6402326E-02 at 30iterations 2.2116015E-05 3.8566589E-03 at 40iterations 1.5396560E-06 2.4795532E-04 at 50iterations finished qdiffx linear iterations at : 06:54:25 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.5396560E-06 2.4795532E-04 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:54:26 3.315u 0.165s 0:03.91 88.7% 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 Tue Oct 11 2011 at 06:54:26 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 = 2903 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: 1.642193 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): -19.94300 45.09200 ymin,ymax (A): 19.25400 75.99500 zmin,zma (A): -70.41300 -20.95200 x,y,z range (A): 65.03500 56.74100 49.46100 scale (grids/A): 1.642193 object centre (A): 12.57450 47.62450 -45.68250 number of atom coordinates read : 2903 total number of charged atoms : 2763 net assigned charge : -1.499988 assigned positive charge : 421.3496 centred at (gu) : 89.68520 89.23515 89.02084 assigned negative charge : -422.8503 centred at (gu) : 89.82611 89.52106 89.10905 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25776 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19840 mr = 42099 m= 2115 mr = 14037 m= 60 mr = 1109 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 27311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 289 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 21167 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) : 0.5473976 object centre at (A) : 12.57450 47.62450 -45.68250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6620205E-03 4.8497804E-03 midg,1,midg; midg,igrid,midg -2.3574724E-03 2.1886979E-03 1,midg,midg; igrid,midg,midg 6.9554145E-03 -1.9322865E-02 gauss-seidel spectral radius is 0.9982050 estimated iterations to convergence 187 setup time was (sec) 0.7500000 now iterating at: 06:54:27 rms-change max change #iterations 3.249679 160.2861 at 10iterations 1.350821 49.68008 at 20iterations 0.5648128 20.76329 at 30iterations 0.2373388 8.230484 at 40iterations 9.8906823E-02 3.449860 at 50iterations 4.1544948E-02 1.581043 at 60iterations 1.7455461E-02 0.6468735 at 70iterations 7.3157726E-03 0.2521667 at 80iterations 3.0615348E-03 0.1145782 at 90iterations 1.2817901E-03 5.2614212E-02 at 100iterations 5.3934293E-04 1.9058228E-02 at 110iterations 2.2582916E-04 8.4552765E-03 at 120iterations finished qdiffx linear iterations at : 06:54:33 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 2.2582916E-04 8.4552765E-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) 7.310000 DelPhi exited at 06:54:34 7.317u 0.200s 0:08.18 91.8% 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 Tue Oct 11 2011 at 06:54:34 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 = 2903 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: 2.463289 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): -19.94300 45.09200 ymin,ymax (A): 19.25400 75.99500 zmin,zma (A): -70.41300 -20.95200 x,y,z range (A): 65.03500 56.74100 49.46100 scale (grids/A): 2.463289 object centre (A): 12.57450 47.62450 -45.68250 number of atom coordinates read : 2903 total number of charged atoms : 2763 net assigned charge : -1.499988 assigned positive charge : 421.3496 centred at (gu) : 89.52759 88.85259 88.53111 assigned negative charge : -422.8503 centred at (gu) : 89.73914 89.28147 88.66352 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 145126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25776 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67876 mr = 102888 m= 20439 mr = 54275 m= 3335 mr = 15857 m= 242 mr = 2277 m= 0 mr = 112 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 61609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 22083 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) : 1.642193 object centre at (A) : 12.57450 47.62450 -45.68250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1162824 9.1237739E-02 midg,1,midg; midg,igrid,midg -1.8664958E-02 5.2069128E-02 1,midg,midg; igrid,midg,midg 0.1187036 -0.2698282 gauss-seidel spectral radius is 0.9991435 estimated iterations to convergence 270 setup time was (sec) 1.380000 now iterating at: 06:54:36 rms-change max change #iterations 8.398457 311.2489 at 10iterations 4.694648 125.7415 at 20iterations 2.623289 65.78056 at 30iterations 1.455053 30.03194 at 40iterations 0.8083127 17.75466 at 50iterations 0.4470862 9.335457 at 60iterations 0.2470772 4.824625 at 70iterations 0.1362918 2.721428 at 80iterations 7.5066060E-02 1.594772 at 90iterations 4.1283909E-02 1.070948 at 100iterations 2.2741638E-02 0.4823856 at 110iterations 1.2521365E-02 0.2728996 at 120iterations 6.8736565E-03 0.1406512 at 130iterations 3.7894256E-03 8.2382202E-02 at 140iterations 2.0828275E-03 4.3205261E-02 at 150iterations 1.1477292E-03 2.2407532E-02 at 160iterations 6.2933500E-04 1.2741089E-02 at 170iterations 3.4679985E-04 6.9322586E-03 at 180iterations finished qdiffx linear iterations at : 06:54:46 total time elapsed so far: 11.51000 # loops : 180 mean,max change (kT/e) : 3.4679985E-04 6.9322586E-03 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 06:54:47 11.694u 0.210s 0:12.24 97.2% 0+0k 0+0io 0pf+0w