Tue Oct 11 03:58:47 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 Tue Oct 11 2011 at 03:58:47 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6632881 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): -12.30500 37.17200 ymin,ymax (A): -27.20100 21.48400 zmin,zma (A): -7.943000 45.72900 x,y,z range (A): 49.47700 48.68500 53.67200 scale (grids/A): 0.6632881 object centre (A): 12.43350 -2.858500 18.89300 number of atom coordinates read : 2679 total number of charged atoms : 2532 net assigned charge : 4.500015 assigned positive charge : 408.9698 centred at (gu) : 90.36206 90.30697 91.23080 assigned negative charge : -404.4704 centred at (gu) : 90.06166 90.11504 91.14768 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7901 nv = 96 ne = 84 npr = 55022 no. pairs analyzed = 55022 no. exposed pairs = 3158 no. arc points = 22166 no. surface atoms = 1061 nbur = 1618 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 4561 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2000000 number of dielectric boundary points 3713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2164 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1236797E-09 3.9310510E-08 midg,1,midg; midg,igrid,midg -2.9867206E-08 5.7690265E-08 1,midg,midg; igrid,midg,midg -5.3228867E-08 8.3265505E-08 gauss-seidel spectral radius is 0.9882220 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 03:58:47 rms-change max change #iterations 0.1782816 24.67466 at 10iterations 1.9442812E-02 2.940262 at 20iterations 2.1252995E-03 0.2678623 at 30iterations 2.2976779E-04 3.0040741E-02 at 40iterations 2.4797391E-05 3.0765533E-03 at 50iterations finished qdiffx linear iterations at : 03:58:50 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.4797391E-05 3.0765533E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:58:51 3.384u 0.176s 0:04.10 86.5% 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 Oct 11 2011 at 03:58:51 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.989864 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): -12.30500 37.17200 ymin,ymax (A): -27.20100 21.48400 zmin,zma (A): -7.943000 45.72900 x,y,z range (A): 49.47700 48.68500 53.67200 scale (grids/A): 1.989864 object centre (A): 12.43350 -2.858500 18.89300 number of atom coordinates read : 2679 total number of charged atoms : 2532 net assigned charge : 4.500015 assigned positive charge : 408.9698 centred at (gu) : 91.08572 90.92007 93.69167 assigned negative charge : -404.4704 centred at (gu) : 90.18491 90.34507 93.44262 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22166 grid for indexing accessible points = 1.400000 m= 32776 mr = 60941 m= 5433 mr = 24809 m= 391 mr = 3529 m= 17 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.4100000 number of dielectric boundary points 34378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20011 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) : 0.6632881 object centre at (A) : 12.43350 -2.858500 18.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6358550E-02 1.1831959E-02 midg,1,midg; midg,igrid,midg -1.2879220E-02 4.5503046E-02 1,midg,midg; igrid,midg,midg -2.4907984E-02 9.5588066E-02 gauss-seidel spectral radius is 0.9987500 estimated iterations to convergence 224 setup time was (sec) 0.6300000 now iterating at: 03:58:52 rms-change max change #iterations 4.756255 183.7554 at 10iterations 2.311696 74.28992 at 20iterations 1.116072 32.37683 at 30iterations 0.5415252 16.21395 at 40iterations 0.2630223 7.569268 at 50iterations 0.1276935 3.628182 at 60iterations 6.1871428E-02 1.654409 at 70iterations 2.9952765E-02 0.8551064 at 80iterations 1.4550995E-02 0.4497452 at 90iterations 7.0513962E-03 0.2112435 at 100iterations 3.4275693E-03 0.1066763 at 110iterations 1.6660931E-03 5.3306580E-02 at 120iterations finished qdiffx linear iterations at : 03:58:59 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.6660931E-03 5.3306580E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 03:58:59 7.790u 0.199s 0:08.51 93.7% 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 03:58:59 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.984797 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): -12.30500 37.17200 ymin,ymax (A): -27.20100 21.48400 zmin,zma (A): -7.943000 45.72900 x,y,z range (A): 49.47700 48.68500 53.67200 scale (grids/A): 2.984797 object centre (A): 12.43350 -2.858500 18.89300 number of atom coordinates read : 2679 total number of charged atoms : 2532 net assigned charge : 4.500015 assigned positive charge : 408.9698 centred at (gu) : 91.62829 91.38012 95.53746 assigned negative charge : -404.4704 centred at (gu) : 90.27728 90.51748 95.16391 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 197086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22166 grid for indexing accessible points = 1.400000 m= 104222 mr = 146909 m= 39728 mr = 86980 m= 10074 mr = 32360 m= 1671 mr = 7695 m= 133 mr = 1157 m= 3 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 1.090000 number of dielectric boundary points 77735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 20256 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) : 1.989864 object centre at (A) : 12.43350 -2.858500 18.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3666855 0.2152414 midg,1,midg; midg,igrid,midg -0.1499055 0.4844670 1,midg,midg; igrid,midg,midg -0.2406717 0.8445243 gauss-seidel spectral radius is 0.9992834 estimated iterations to convergence 295 setup time was (sec) 1.320000 now iterating at: 03:59:01 rms-change max change #iterations 10.94290 433.4280 at 10iterations 6.415796 135.7622 at 20iterations 3.763845 72.41980 at 30iterations 2.197065 43.22992 at 40iterations 1.281152 24.02722 at 50iterations 0.7482591 13.84679 at 60iterations 0.4365094 7.846351 at 70iterations 0.2535239 4.605072 at 80iterations 0.1478257 2.560108 at 90iterations 8.5981503E-02 1.414882 at 100iterations 4.9929854E-02 0.8321075 at 110iterations 2.8966567E-02 0.5462646 at 120iterations 1.6860485E-02 0.2749290 at 130iterations 9.8096989E-03 0.1582642 at 140iterations 5.6887879E-03 9.1976166E-02 at 150iterations 3.3164949E-03 6.1420441E-02 at 160iterations 1.9279107E-03 3.3185959E-02 at 170iterations 1.1269341E-03 1.8989563E-02 at 180iterations finished qdiffx linear iterations at : 03:59:12 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 1.1269341E-03 1.8989563E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 03:59:13 12.728u 0.233s 0:13.42 96.4% 0+0k 0+0io 0pf+0w