Sat Oct 15 12:25:06 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 Sat Oct 15 2011 at 12:25:06 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4531 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4198410 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): -53.94800 3.388000 ymin,ymax (A): 17.85100 84.64600 zmin,zma (A): -42.94200 41.85200 x,y,z range (A): 57.33600 66.79500 84.79401 scale (grids/A): 0.4198410 object centre (A): -25.28000 51.24850 -0.5450001 number of atom coordinates read : 4531 total number of charged atoms : 4303 net assigned charge : 19.29999 assigned positive charge : 665.0291 centred at (gu) : 89.99813 91.59274 93.73869 assigned negative charge : -645.7336 centred at (gu) : 90.01797 91.55770 93.78196 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 4785 nv = 96 ne = 84 npr = 90668 no. pairs analyzed = 90668 no. exposed pairs = 5815 no. arc points = 40742 no. surface atoms = 1967 nbur = 2564 mkacc time = 0.3100000 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 = 2.016000 m= 120 mr = 2237 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 0.6000000 number of dielectric boundary points 2668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3230 ## 732 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 6514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1720978E-13 3.4838799E-12 midg,1,midg; midg,igrid,midg 7.9475342E-13 4.4720516E-12 1,midg,midg; igrid,midg,midg 2.4033718E-12 1.5925291E-12 gauss-seidel spectral radius is 0.9710965 estimated iterations to convergence 49 setup time was (sec) 0.9000000 now iterating at: 12:25:07 rms-change max change #iterations 2.5312465E-02 9.163430 at 10iterations 3.3914112E-03 0.6475563 at 20iterations 1.0531549E-03 0.2141705 at 30iterations 3.4018426E-04 6.9843292E-02 at 40iterations 1.1033266E-04 2.2724152E-02 at 50iterations finished qdiffx linear iterations at : 12:25:12 total time elapsed so far: 5.450000 # loops : 50 mean,max change (kT/e) : 1.1033266E-04 2.2724152E-02 energy calculations done at 5.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.660000 DelPhi exited at 12:25:12 5.664u 0.447s 0:06.54 93.2% 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 12:25:12 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4531 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.259523 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): -53.94800 3.388000 ymin,ymax (A): 17.85100 84.64600 zmin,zma (A): -42.94200 41.85200 x,y,z range (A): 57.33600 66.79500 84.79401 scale (grids/A): 1.259523 object centre (A): -25.28000 51.24850 -0.5450001 number of atom coordinates read : 4531 total number of charged atoms : 4303 net assigned charge : 19.29999 assigned positive charge : 665.0291 centred at (gu) : 89.99282 94.77638 101.2142 assigned negative charge : -645.7336 centred at (gu) : 90.05341 94.67260 101.3454 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 56553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40742 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 12685 mr = 37017 m= 572 mr = 7432 m= 3 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 201 time to turn everything in is 0.6600000 number of dielectric boundary points 25270 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 791 ## 29 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 29541 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) : 0.4198410 object centre at (A) : -25.28000 51.24850 -0.5450001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2067143E-03 1.4218357E-02 midg,1,midg; midg,igrid,midg 1.3670913E-03 3.9001489E-03 1,midg,midg; igrid,midg,midg 8.3565275E-04 9.7747566E-04 gauss-seidel spectral radius is 0.9970228 estimated iterations to convergence 146 setup time was (sec) 1.000000 now iterating at: 12:25:14 rms-change max change #iterations 2.196914 110.1799 at 10iterations 0.7203588 31.98929 at 20iterations 0.2375532 10.22191 at 30iterations 7.8358866E-02 3.328575 at 40iterations 2.6254248E-02 1.054514 at 50iterations 9.3252473E-03 0.4150658 at 60iterations 3.9251535E-03 0.1786642 at 70iterations 2.0920895E-03 0.1004829 at 80iterations 1.3290319E-03 6.1096191E-02 at 90iterations 8.9332531E-04 4.0479660E-02 at 100iterations 6.0924410E-04 2.7496338E-02 at 110iterations 4.1814675E-04 1.8772125E-02 at 120iterations finished qdiffx linear iterations at : 12:25:24 total time elapsed so far: 10.96000 # loops : 120 mean,max change (kT/e) : 4.1814675E-04 1.8772125E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.17000 DelPhi exited at 12:25:24 11.179u 0.515s 0:11.99 97.4% 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 12:25:24 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4531 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.889284 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): -53.94800 3.388000 ymin,ymax (A): 17.85100 84.64600 zmin,zma (A): -42.94200 41.85200 x,y,z range (A): 57.33600 66.79500 84.79401 scale (grids/A): 1.889284 object centre (A): -25.28000 51.24850 -0.5450001 number of atom coordinates read : 4531 total number of charged atoms : 4303 net assigned charge : 19.29999 assigned positive charge : 665.0291 centred at (gu) : 89.98872 97.16419 106.8210 assigned negative charge : -645.7336 centred at (gu) : 90.07997 97.00886 107.0182 start vw surface at 0.2200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 132901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40742 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 49795 mr = 92579 m= 8618 mr = 36529 m= 523 mr = 5411 m= 6 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 679 time to turn everything in is 1.520000 number of dielectric boundary points 57170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 33813 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) : 1.259523 object centre at (A) : -25.28000 51.24850 -0.5450001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5990450E-02 0.3867042 midg,1,midg; midg,igrid,midg 3.9501872E-02 0.1049813 1,midg,midg; igrid,midg,midg 1.6387360E-02 2.7257541E-02 gauss-seidel spectral radius is 0.9987687 estimated iterations to convergence 226 setup time was (sec) 1.910000 now iterating at: 12:25:27 rms-change max change #iterations 6.758724 226.7337 at 10iterations 3.413823 106.7088 at 20iterations 1.708832 48.37554 at 30iterations 0.8499396 21.78012 at 40iterations 0.4219495 10.86950 at 50iterations 0.2083489 5.444317 at 60iterations 0.1026998 2.559929 at 70iterations 5.0456945E-02 1.310558 at 80iterations 2.4830569E-02 0.6473427 at 90iterations 1.2239572E-02 0.3383598 at 100iterations 6.0324678E-03 0.1660538 at 110iterations 3.0123773E-03 7.4096680E-02 at 120iterations 1.5394993E-03 4.0599823E-02 at 130iterations 8.2629872E-04 2.2281647E-02 at 140iterations 4.7828452E-04 1.3259888E-02 at 150iterations 3.0587180E-04 8.6059570E-03 at 160iterations 2.1173108E-04 5.5007935E-03 at 170iterations 1.5567662E-04 4.0092468E-03 at 180iterations finished qdiffx linear iterations at : 12:25:43 total time elapsed so far: 18.42000 # loops : 180 mean,max change (kT/e) : 1.5567662E-04 4.0092468E-03 energy calculations done at 18.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.64000 DelPhi exited at 12:25:44 18.650u 0.494s 0:19.49 98.2% 0+0k 0+0io 0pf+0w