Sat Oct 8 11:35:56 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 8 2011 at 11:35:56 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4211 !!! WARNING: SEP 291 has a net charge of -0.4750 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: 0.5239686 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): -2.302000 65.64100 ymin,ymax (A): -11.40500 37.95600 zmin,zma (A): -21.62300 44.26600 x,y,z range (A): 67.94300 49.36100 65.88900 scale (grids/A): 0.5239686 object centre (A): 31.66950 13.27550 11.32150 number of atom coordinates read : 4211 total number of charged atoms : 4045 net assigned charge : -8.974956 assigned positive charge : 630.3340 centred at (gu) : 88.01025 90.24677 90.84957 assigned negative charge : -639.3115 centred at (gu) : 88.05867 90.33120 90.89420 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6630 nv = 96 ne = 84 npr = 93744 no. pairs analyzed = 93744 no. exposed pairs = 4396 no. arc points = 29972 no. surface atoms = 1491 nbur = 2720 mkacc time = 0.2100000 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 = 1.624000 m= 198 mr = 3705 m= 0 mr = 5 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.4300000 number of dielectric boundary points 3118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3000 ## 426 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9306 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1317880E-11 -5.0844584E-10 midg,1,midg; midg,igrid,midg 1.0105619E-10 -6.0959798E-10 1,midg,midg; igrid,midg,midg -4.8896855E-11 -2.5698815E-10 gauss-seidel spectral radius is 0.9813036 estimated iterations to convergence 60 setup time was (sec) 0.6700000 now iterating at: 11:35:56 rms-change max change #iterations 7.3224455E-02 10.01591 at 10iterations 4.5989929E-03 0.7236142 at 20iterations 3.6539996E-04 5.9467316E-02 at 30iterations 4.6682628E-05 9.4661713E-03 at 40iterations 7.7804543E-06 1.6708374E-03 at 50iterations finished qdiffx linear iterations at : 11:35:59 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 7.7804543E-06 1.6708374E-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) 3.520000 DelPhi exited at 11:36:00 3.519u 0.157s 0:04.49 81.5% 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 Sat Oct 8 2011 at 11:36:00 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4211 !!! WARNING: SEP 291 has a net charge of -0.4750 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: 1.571906 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): -2.302000 65.64100 ymin,ymax (A): -11.40500 37.95600 zmin,zma (A): -21.62300 44.26600 x,y,z range (A): 67.94300 49.36100 65.88900 scale (grids/A): 1.571906 object centre (A): 31.66950 13.27550 11.32150 number of atom coordinates read : 4211 total number of charged atoms : 4045 net assigned charge : -8.974956 assigned positive charge : 630.3340 centred at (gu) : 84.02954 90.73920 92.54765 assigned negative charge : -639.3115 centred at (gu) : 84.17568 90.99330 92.68233 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 76522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29972 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20324 mr = 54941 m= 1786 mr = 13767 m= 40 mr = 815 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 5432 time to turn everything in is 0.5500000 number of dielectric boundary points 29149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 30607 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) : 0.5239686 object centre at (A) : 31.66950 13.27550 11.32150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9441996E-03 -1.6247489E-02 midg,1,midg; midg,igrid,midg -3.5488557E-03 -1.1870058E-02 1,midg,midg; igrid,midg,midg 1.4152864E-02 -8.3186552E-03 gauss-seidel spectral radius is 0.9981214 estimated iterations to convergence 183 setup time was (sec) 0.8300000 now iterating at: 11:36:01 rms-change max change #iterations 3.736559 164.8333 at 10iterations 1.527832 49.35352 at 20iterations 0.6318084 21.06696 at 30iterations 0.2591243 8.640121 at 40iterations 0.1069347 3.516462 at 50iterations 4.4139791E-02 1.415765 at 60iterations 1.8194309E-02 0.6060889 at 70iterations 7.4981116E-03 0.2767525 at 80iterations 3.1004760E-03 0.1053467 at 90iterations 1.2758839E-03 4.1580200E-02 at 100iterations 5.2915607E-04 1.6971588E-02 at 110iterations 2.1836226E-04 7.1430206E-03 at 120iterations finished qdiffx linear iterations at : 11:36:08 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 2.1836226E-04 7.1430206E-03 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 11:36:08 7.520u 0.177s 0:07.99 96.2% 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 8 2011 at 11:36:08 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4211 !!! WARNING: SEP 291 has a net charge of -0.4750 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: 2.357859 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): -2.302000 65.64100 ymin,ymax (A): -11.40500 37.95600 zmin,zma (A): -21.62300 44.26600 x,y,z range (A): 67.94300 49.36100 65.88900 scale (grids/A): 2.357859 object centre (A): 31.66950 13.27550 11.32150 number of atom coordinates read : 4211 total number of charged atoms : 4045 net assigned charge : -8.974956 assigned positive charge : 630.3340 centred at (gu) : 81.04401 91.10863 93.82122 assigned negative charge : -639.3115 centred at (gu) : 81.26337 91.48978 94.02338 start vw surface at 0.1900000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 179317 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29972 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 74798 mr = 134823 m= 18330 mr = 59237 m= 2569 mr = 13607 m= 141 mr = 1569 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 17966 time to turn everything in is 1.300000 number of dielectric boundary points 65869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 32309 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) : 1.571906 object centre at (A) : 31.66950 13.27550 11.32150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2671958 -0.2872072 midg,1,midg; midg,igrid,midg -7.5138584E-02 -0.1827692 1,midg,midg; igrid,midg,midg 0.5684618 -0.3968453 gauss-seidel spectral radius is 0.9991310 estimated iterations to convergence 268 setup time was (sec) 1.590000 now iterating at: 11:36:10 rms-change max change #iterations 9.706020 292.1933 at 10iterations 5.388601 136.6388 at 20iterations 2.979983 59.89778 at 30iterations 1.650043 34.80685 at 40iterations 0.9085312 18.11905 at 50iterations 0.4987739 10.01220 at 60iterations 0.2747599 5.640753 at 70iterations 0.1509320 2.728886 at 80iterations 8.2892999E-02 1.620180 at 90iterations 4.5656089E-02 0.8617582 at 100iterations 2.5035933E-02 0.4616241 at 110iterations 1.3765437E-02 0.2709937 at 120iterations 7.5411405E-03 0.1407781 at 130iterations 4.1342638E-03 7.7850342E-02 at 140iterations 2.2698564E-03 4.0023804E-02 at 150iterations 1.2447604E-03 2.2972107E-02 at 160iterations 6.8443140E-04 1.3868332E-02 at 170iterations 3.7458874E-04 7.5988770E-03 at 180iterations finished qdiffx linear iterations at : 11:36:20 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 3.7458874E-04 7.5988770E-03 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 11:36:21 12.102u 0.187s 0:12.57 97.6% 0+0k 0+0io 0pf+0w