Mon Oct 10 17:02:57 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 Mon Oct 10 2011 at 17:02:57 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 = 3269 !!! WARNING: HIR 201 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5775658 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): -50.84300 7.059000 ymin,ymax (A): 37.69900 93.51400 zmin,zma (A): -4.582000 57.05600 x,y,z range (A): 57.90200 55.81500 61.63800 scale (grids/A): 0.5775658 object centre (A): -21.89200 65.60650 26.23700 number of atom coordinates read : 3269 total number of charged atoms : 3130 net assigned charge : 7.514017 assigned positive charge : 500.3308 centred at (gu) : 89.88854 90.86399 87.87143 assigned negative charge : -492.8177 centred at (gu) : 89.89521 90.93729 87.87294 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7149 nv = 96 ne = 84 npr = 66115 no. pairs analyzed = 66115 no. exposed pairs = 4026 no. arc points = 28667 no. surface atoms = 1355 nbur = 1914 mkacc time = 0.1100000 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 = 1.512000 m= 312 mr = 3823 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2300000 number of dielectric boundary points 3612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 381 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9134 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5307103E-09 9.1793873E-10 midg,1,midg; midg,igrid,midg 2.5683520E-09 -1.9065655E-10 1,midg,midg; igrid,midg,midg 1.7064410E-09 1.3311813E-09 gauss-seidel spectral radius is 0.9845514 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 17:02:58 rms-change max change #iterations 0.1032741 15.89905 at 10iterations 8.1023574E-03 1.366158 at 20iterations 6.1771448E-04 8.9695930E-02 at 30iterations 4.8044807E-05 6.8664551E-03 at 40iterations 3.7425957E-06 5.3930283E-04 at 50iterations finished qdiffx linear iterations at : 17:03:01 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.7425957E-06 5.3930283E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 17:03:02 3.400u 0.142s 0:04.60 76.9% 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 Mon Oct 10 2011 at 17:03:02 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 = 3269 !!! WARNING: HIR 201 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.732697 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): -50.84300 7.059000 ymin,ymax (A): 37.69900 93.51400 zmin,zma (A): -4.582000 57.05600 x,y,z range (A): 57.90200 55.81500 61.63800 scale (grids/A): 1.732697 object centre (A): -21.89200 65.60650 26.23700 number of atom coordinates read : 3269 total number of charged atoms : 3130 net assigned charge : 7.514017 assigned positive charge : 500.3308 centred at (gu) : 89.66489 92.59088 83.61315 assigned negative charge : -492.8177 centred at (gu) : 89.68539 92.81147 83.61816 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28667 grid for indexing accessible points = 1.400000 m= 25896 mr = 52948 m= 3043 mr = 18498 m= 97 mr = 1672 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1596 time to turn everything in is 0.3800000 number of dielectric boundary points 33692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 24283 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) : 0.5775658 object centre at (A) : -21.89200 65.60650 26.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6733356E-04 1.7391969E-02 midg,1,midg; midg,igrid,midg 2.3858530E-02 7.7279485E-03 1,midg,midg; igrid,midg,midg 1.7361550E-03 3.3052735E-02 gauss-seidel spectral radius is 0.9984174 estimated iterations to convergence 199 setup time was (sec) 0.5900000 now iterating at: 17:03:03 rms-change max change #iterations 3.996384 160.0708 at 10iterations 1.755032 60.96017 at 20iterations 0.7707787 25.86490 at 30iterations 0.3408955 11.32363 at 40iterations 0.1507367 4.814517 at 50iterations 6.6559017E-02 2.147625 at 60iterations 2.9351635E-02 0.9347124 at 70iterations 1.2972963E-02 0.4260235 at 80iterations 5.7124188E-03 0.1765710 at 90iterations 2.5294276E-03 8.1489086E-02 at 100iterations 1.1176136E-03 3.6342621E-02 at 110iterations 4.9355760E-04 1.7132878E-02 at 120iterations finished qdiffx linear iterations at : 17:03:10 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 4.9355760E-04 1.7132878E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 17:03:10 7.678u 0.200s 0:08.47 92.9% 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 Mon Oct 10 2011 at 17:03:11 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 = 3269 !!! WARNING: HIR 201 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.599046 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): -50.84300 7.059000 ymin,ymax (A): 37.69900 93.51400 zmin,zma (A): -4.582000 57.05600 x,y,z range (A): 57.90200 55.81500 61.63800 scale (grids/A): 2.599046 object centre (A): -21.89200 65.60650 26.23700 number of atom coordinates read : 3269 total number of charged atoms : 3130 net assigned charge : 7.514017 assigned positive charge : 500.3308 centred at (gu) : 89.49683 93.88622 80.41960 assigned negative charge : -492.8177 centred at (gu) : 89.52795 94.21703 80.42710 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 180169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28667 grid for indexing accessible points = 1.400000 m= 87015 mr = 128987 m= 26937 mr = 70040 m= 5038 mr = 20828 m= 493 mr = 3568 m= 17 mr = 282 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 5534 time to turn everything in is 0.9300000 number of dielectric boundary points 75964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 25034 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) : 1.732697 object centre at (A) : -21.89200 65.60650 26.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1184477E-02 0.1744899 midg,1,midg; midg,igrid,midg 0.3202416 6.3680224E-02 1,midg,midg; igrid,midg,midg -3.2760967E-02 0.5111962 gauss-seidel spectral radius is 0.9992144 estimated iterations to convergence 282 setup time was (sec) 1.170000 now iterating at: 17:03:12 rms-change max change #iterations 9.948616 282.5269 at 10iterations 5.687093 152.8376 at 20iterations 3.238611 62.40563 at 30iterations 1.842517 41.18121 at 40iterations 1.043141 19.89977 at 50iterations 0.5897937 11.07190 at 60iterations 0.3329425 6.803322 at 70iterations 0.1884397 3.525305 at 80iterations 0.1064199 1.896149 at 90iterations 5.9947647E-02 1.083905 at 100iterations 3.3878740E-02 0.6202927 at 110iterations 1.9104965E-02 0.3394699 at 120iterations 1.0774292E-02 0.1862559 at 130iterations 6.0804789E-03 0.1106694 at 140iterations 3.4281847E-03 6.1248779E-02 at 150iterations 1.9326617E-03 4.0351868E-02 at 160iterations 1.0923911E-03 2.0200729E-02 at 170iterations 6.1633828E-04 1.1131287E-02 at 180iterations finished qdiffx linear iterations at : 17:03:23 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 6.1633828E-04 1.1131287E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 17:03:24 12.453u 0.220s 0:13.13 96.4% 0+0k 0+0io 0pf+0w