Sat Oct 15 10:23:19 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 15 2011 at 10:23:19 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5779971 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): -27.35300 34.23900 ymin,ymax (A): 35.31900 95.00500 zmin,zma (A): 30.95800 89.37500 x,y,z range (A): 61.59200 59.68600 58.41700 scale (grids/A): 0.5779971 object centre (A): 3.443001 65.16200 60.16650 number of atom coordinates read : 4417 total number of charged atoms : 4256 net assigned charge : -8.485952 assigned positive charge : 664.9402 centred at (gu) : 90.77655 88.99373 89.14745 assigned negative charge : -673.4293 centred at (gu) : 90.62608 89.04057 89.30670 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9456 nv = 96 ne = 84 npr = 92825 no. pairs analyzed = 92825 no. exposed pairs = 4971 no. arc points = 33290 no. surface atoms = 1676 nbur = 2741 mkacc time = 0.2000000 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 = 1.484000 m= 409 mr = 5537 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 116 time to turn everything in is 0.4300000 number of dielectric boundary points 4290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3484 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 12392 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7604906E-09 -5.6298672E-09 midg,1,midg; midg,igrid,midg -4.4597798E-10 -2.6057949E-09 1,midg,midg; igrid,midg,midg -5.4949987E-09 3.3725727E-09 gauss-seidel spectral radius is 0.9846534 estimated iterations to convergence 66 setup time was (sec) 0.6800000 now iterating at: 10:23:20 rms-change max change #iterations 0.1232692 16.67210 at 10iterations 9.8741483E-03 1.361597 at 20iterations 1.0625923E-03 0.1402583 at 30iterations 2.4162896E-04 2.8181076E-02 at 40iterations 8.4010862E-05 1.0677338E-02 at 50iterations finished qdiffx linear iterations at : 10:23:23 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 8.4010862E-05 1.0677338E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 10:23:24 3.606u 0.214s 0:04.42 86.1% 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 Sat Oct 15 2011 at 10:23:24 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.733991 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): -27.35300 34.23900 ymin,ymax (A): 35.31900 95.00500 zmin,zma (A): 30.95800 89.37500 x,y,z range (A): 61.59200 59.68600 58.41700 scale (grids/A): 1.733991 object centre (A): 3.443001 65.16200 60.16650 number of atom coordinates read : 4417 total number of charged atoms : 4256 net assigned charge : -8.485952 assigned positive charge : 664.9402 centred at (gu) : 92.32832 86.97978 87.44095 assigned negative charge : -673.4293 centred at (gu) : 91.87786 87.12121 87.91965 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 105945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33290 grid for indexing accessible points = 1.400000 m= 36300 mr = 77549 m= 4670 mr = 26993 m= 164 mr = 2865 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 6236 time to turn everything in is 0.7100000 number of dielectric boundary points 39626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 33023 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) : 0.5779971 object centre at (A) : 3.443001 65.16200 60.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6020607E-02 -3.2433148E-02 midg,1,midg; midg,igrid,midg 1.1780377E-02 -2.1112779E-02 1,midg,midg; igrid,midg,midg -3.9059490E-02 3.5294831E-02 gauss-seidel spectral radius is 0.9985170 estimated iterations to convergence 206 setup time was (sec) 1.030000 now iterating at: 10:23:25 rms-change max change #iterations 4.810045 172.8024 at 10iterations 2.170654 67.25432 at 20iterations 0.9877653 29.51181 at 30iterations 0.4482025 12.72654 at 40iterations 0.2035650 6.119709 at 50iterations 9.2738792E-02 2.531876 at 60iterations 4.2231128E-02 1.181557 at 70iterations 1.9240901E-02 0.5334015 at 80iterations 8.8088885E-03 0.2480230 at 90iterations 4.0331702E-03 0.1119738 at 100iterations 1.8695141E-03 5.4870605E-02 at 110iterations 8.8765071E-04 2.4554253E-02 at 120iterations finished qdiffx linear iterations at : 10:23:32 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 8.8765071E-04 2.4554253E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 10:23:33 8.206u 0.256s 0:09.08 93.0% 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 Sat Oct 15 2011 at 10:23:33 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.600987 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): -27.35300 34.23900 ymin,ymax (A): 35.31900 95.00500 zmin,zma (A): 30.95800 89.37500 x,y,z range (A): 61.59200 59.68600 58.41700 scale (grids/A): 2.600987 object centre (A): 3.443001 65.16200 60.16650 number of atom coordinates read : 4417 total number of charged atoms : 4256 net assigned charge : -8.485952 assigned positive charge : 664.9402 centred at (gu) : 93.49208 85.46940 86.16100 assigned negative charge : -673.4293 centred at (gu) : 92.81654 85.68173 86.87952 start vw surface at 0.1800000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 246301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33290 grid for indexing accessible points = 1.400000 m= 122976 mr = 187929 m= 39223 mr = 101949 m= 7944 mr = 31381 m= 749 mr = 6025 m= 12 mr = 458 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 20806 time to turn everything in is 1.810000 number of dielectric boundary points 89463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 34031 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) : 1.733991 object centre at (A) : 3.443001 65.16200 60.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6408349 -0.3760159 midg,1,midg; midg,igrid,midg 0.2575390 -0.4327896 1,midg,midg; igrid,midg,midg -0.3905358 0.3853017 gauss-seidel spectral radius is 0.9992521 estimated iterations to convergence 289 setup time was (sec) 2.150000 now iterating at: 10:23:35 rms-change max change #iterations 11.70337 332.0189 at 10iterations 6.842707 138.5631 at 20iterations 3.958386 71.19278 at 30iterations 2.293326 37.84867 at 40iterations 1.321473 27.23602 at 50iterations 0.7618405 12.55556 at 60iterations 0.4404445 7.495625 at 70iterations 0.2527510 4.374371 at 80iterations 0.1451886 2.496228 at 90iterations 8.3559945E-02 1.444549 at 100iterations 4.7994908E-02 0.8461170 at 110iterations 2.7646478E-02 0.4583454 at 120iterations 1.5919121E-02 0.2586098 at 130iterations 9.1848699E-03 0.1470699 at 140iterations 5.3443876E-03 8.1951141E-02 at 150iterations 3.1362290E-03 4.9706936E-02 at 160iterations 1.8771080E-03 3.3927917E-02 at 170iterations 1.1594939E-03 2.2155762E-02 at 180iterations finished qdiffx linear iterations at : 10:23:47 total time elapsed so far: 13.94000 # loops : 180 mean,max change (kT/e) : 1.1594939E-03 2.2155762E-02 energy calculations done at 13.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.12000 DelPhi exited at 10:23:48 14.117u 0.270s 0:14.74 97.5% 0+0k 0+0io 0pf+0w