Tue Nov 22 14:11:44 PST 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 Tue Nov 22 2011 at 14:11:50 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6400000 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): -5.196000 34.97100 ymin,ymax (A): -3.632000 49.20300 zmin,zma (A): -24.41900 31.20600 x,y,z range (A): 40.16700 52.83500 55.62500 scale (grids/A): 0.6400000 object centre (A): 14.88750 22.78550 3.393501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 90.62262 92.31751 90.12952 assigned negative charge : -288.4263 centred at (gu) : 90.72533 92.43804 90.09203 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5523 nv = 96 ne = 84 npr = 40170 no. pairs analyzed = 40170 no. exposed pairs = 2456 no. arc points = 17362 no. surface atoms = 826 nbur = 1138 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 274 mr = 3093 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.1600000 number of dielectric boundary points 2675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1705 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6462 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4066956E-09 8.1136493E-09 midg,1,midg; midg,igrid,midg 9.1341423E-09 -9.9510871E-09 1,midg,midg; igrid,midg,midg 1.1751819E-08 -4.9204023E-09 gauss-seidel spectral radius is 0.9872953 estimated iterations to convergence 73 setup time was (sec) 0.3500000 now iterating at: 14:11:53 rms-change max change #iterations 0.1284093 25.22243 at 10iterations 1.2610400E-02 2.456242 at 20iterations 1.2593060E-03 0.1919255 at 30iterations 1.2139241E-04 1.8402100E-02 at 40iterations 1.2094808E-05 2.0675659E-03 at 50iterations finished qdiffx linear iterations at : 14:12:02 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.2094808E-05 2.0675659E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:12:04 3.456u 0.199s 0:14.82 24.5% 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 Nov 22 2011 at 14:12:07 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.920000 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): -5.196000 34.97100 ymin,ymax (A): -3.632000 49.20300 zmin,zma (A): -24.41900 31.20600 x,y,z range (A): 40.16700 52.83500 55.62500 scale (grids/A): 1.920000 object centre (A): 14.88750 22.78550 3.393501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 91.86801 96.95225 90.38840 assigned negative charge : -288.4263 centred at (gu) : 92.17606 97.31447 90.27627 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59201 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 22217 mr = 40970 m= 3579 mr = 17089 m= 165 mr = 2416 m= 0 mr = 65 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1159 time to turn everything in is 0.3200000 number of dielectric boundary points 24622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14433 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) : 0.6400000 object centre at (A) : 14.88750 22.78550 3.393501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5528587E-02 9.8105958E-03 midg,1,midg; midg,igrid,midg 3.1372380E-02 -5.9455698E-03 1,midg,midg; igrid,midg,midg 8.8891769E-03 -4.1872128E-03 gauss-seidel spectral radius is 0.9985797 estimated iterations to convergence 210 setup time was (sec) 0.5700000 now iterating at: 14:12:09 rms-change max change #iterations 3.660294 157.7439 at 10iterations 1.690314 62.23058 at 20iterations 0.7835717 28.27893 at 30iterations 0.3629217 12.69940 at 40iterations 0.1659954 5.864720 at 50iterations 7.6537438E-02 2.654671 at 60iterations 3.5299946E-02 1.211153 at 70iterations 1.6264636E-02 0.5452871 at 80iterations 7.5054346E-03 0.2774119 at 90iterations 3.4722742E-03 0.1275613 at 100iterations 1.5986970E-03 5.3541183E-02 at 110iterations 7.3735521E-04 2.2953033E-02 at 120iterations finished qdiffx linear iterations at : 14:12:30 total time elapsed so far: 8.670000 # loops : 120 mean,max change (kT/e) : 7.3735521E-04 2.2953033E-02 energy calculations done at 8.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 14:12:32 8.797u 0.270s 0:25.33 35.7% 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 Nov 22 2011 at 14:12:35 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.880000 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): -5.196000 34.97100 ymin,ymax (A): -3.632000 49.20300 zmin,zma (A): -24.41900 31.20600 x,y,z range (A): 40.16700 52.83500 55.62500 scale (grids/A): 2.880000 object centre (A): 14.88750 22.78550 3.393501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 92.80201 100.4284 90.58261 assigned negative charge : -288.4263 centred at (gu) : 93.26406 100.9716 90.41454 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 136892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17362 grid for indexing accessible points = 1.400000 m= 70860 mr = 99137 m= 27194 mr = 59062 m= 6619 mr = 22816 m= 851 mr = 5327 m= 47 mr = 584 m= 0 mr = 23 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 3903 time to turn everything in is 0.8200000 number of dielectric boundary points 55514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14656 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) : 1.920000 object centre at (A) : 14.88750 22.78550 3.393501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.074644 6.8850229E-03 midg,1,midg; midg,igrid,midg 0.3354072 -9.5215634E-02 1,midg,midg; igrid,midg,midg 5.8571044E-02 -2.5997562E-02 gauss-seidel spectral radius is 0.9992301 estimated iterations to convergence 285 setup time was (sec) 1.080000 now iterating at: 14:12:42 rms-change max change #iterations 8.651524 340.9915 at 10iterations 4.960464 116.0450 at 20iterations 2.821475 68.25509 at 30iterations 1.604361 31.44372 at 40iterations 0.9100949 18.58252 at 50iterations 0.5165672 10.89017 at 60iterations 0.2923461 6.354149 at 70iterations 0.1662442 3.157028 at 80iterations 9.3952574E-02 2.081651 at 90iterations 5.3310931E-02 1.051304 at 100iterations 3.0172495E-02 0.6493340 at 110iterations 1.7136633E-02 0.3458424 at 120iterations 9.6855294E-03 0.1760602 at 130iterations 5.5024363E-03 0.1116438 at 140iterations 3.1221537E-03 5.9708595E-02 at 150iterations 1.7689784E-03 3.6808014E-02 at 160iterations 9.9970738E-04 2.0816803E-02 at 170iterations 5.6737661E-04 1.2212753E-02 at 180iterations finished qdiffx linear iterations at : 14:13:23 total time elapsed so far: 14.35000 # loops : 180 mean,max change (kT/e) : 5.6737661E-04 1.2212753E-02 energy calculations done at 14.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.49000 DelPhi exited at 14:13:24 14.489u 0.256s 0:49.48 29.7% 0+0k 0+0io 0pf+0w