Sun Oct 9 08:49:07 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 Sun Oct 9 2011 at 08:49:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4798685 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): 3.860000 78.04700 ymin,ymax (A): 22.58000 84.26600 zmin,zma (A): 6.549000 68.81800 x,y,z range (A): 74.18700 61.68600 62.26900 scale (grids/A): 0.4798685 object centre (A): 40.95350 53.42300 37.68350 number of atom coordinates read : 6037 total number of charged atoms : 5869 net assigned charge : -0.9999486 assigned positive charge : 909.2159 centred at (gu) : 90.43906 89.24310 89.33852 assigned negative charge : -910.2237 centred at (gu) : 90.31203 89.23289 89.21709 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8583 nv = 96 ne = 84 npr = 121700 no. pairs analyzed = 121700 no. exposed pairs = 7550 no. arc points = 52045 no. surface atoms = 2517 nbur = 3520 mkacc time = 0.2000000 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 = 1.792000 m= 280 mr = 4387 m= 0 mr = 8 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4899 ## 833 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 11719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2523287E-10 7.8457220E-11 midg,1,midg; midg,igrid,midg -1.3909430E-11 4.3697658E-12 1,midg,midg; igrid,midg,midg -9.5838608E-11 1.1213690E-10 gauss-seidel spectral radius is 0.9778935 estimated iterations to convergence 56 setup time was (sec) 0.5800000 now iterating at: 08:49:08 rms-change max change #iterations 5.4076776E-02 9.956284 at 10iterations 2.5953667E-03 0.4531403 at 20iterations 1.4584091E-04 2.3097992E-02 at 30iterations 1.9811960E-05 4.0693283E-03 at 40iterations 5.0588874E-06 8.5401535E-04 at 50iterations finished qdiffx linear iterations at : 08:49:11 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 5.0588874E-06 8.5401535E-04 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 08:49:11 3.586u 0.171s 0:04.03 93.0% 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 Sun Oct 9 2011 at 08:49:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.439605 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): 3.860000 78.04700 ymin,ymax (A): 22.58000 84.26600 zmin,zma (A): 6.549000 68.81800 x,y,z range (A): 74.18700 61.68600 62.26900 scale (grids/A): 1.439605 object centre (A): 40.95350 53.42300 37.68350 number of atom coordinates read : 6037 total number of charged atoms : 5869 net assigned charge : -0.9999486 assigned positive charge : 909.2159 centred at (gu) : 91.31533 87.72749 88.01411 assigned negative charge : -910.2237 centred at (gu) : 90.93575 87.69830 87.65116 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 98847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52045 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 25890 mr = 67446 m= 1711 mr = 16433 m= 20 mr = 590 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1084 time to turn everything in is 0.4700000 number of dielectric boundary points 41999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 842 ## 17 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 43011 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) : 0.4798685 object centre at (A) : 40.95350 53.42300 37.68350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3789830E-03 1.0505388E-02 midg,1,midg; midg,igrid,midg -1.3495665E-03 -2.5257783E-03 1,midg,midg; igrid,midg,midg -7.4914494E-03 1.3105904E-02 gauss-seidel spectral radius is 0.9979427 estimated iterations to convergence 175 setup time was (sec) 0.6900000 now iterating at: 08:49:12 rms-change max change #iterations 3.761086 169.3171 at 10iterations 1.477879 52.97062 at 20iterations 0.5826466 17.98018 at 30iterations 0.2303919 7.233671 at 40iterations 9.0889148E-02 2.689654 at 50iterations 3.6016747E-02 1.168856 at 60iterations 1.4215368E-02 0.4913940 at 70iterations 5.6572822E-03 0.1774769 at 80iterations 2.2522167E-03 7.5717926E-02 at 90iterations 9.0181030E-04 2.7313232E-02 at 100iterations 3.6758801E-04 1.2544632E-02 at 110iterations 1.5670677E-04 5.2928925E-03 at 120iterations finished qdiffx linear iterations at : 08:49:19 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.5670677E-04 5.2928925E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 08:49:20 7.842u 0.208s 0:08.31 96.7% 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 Sun Oct 9 2011 at 08:49:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6037 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: 2.159408 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): 3.860000 78.04700 ymin,ymax (A): 22.58000 84.26600 zmin,zma (A): 6.549000 68.81800 x,y,z range (A): 74.18700 61.68600 62.26900 scale (grids/A): 2.159408 object centre (A): 40.95350 53.42300 37.68350 number of atom coordinates read : 6037 total number of charged atoms : 5869 net assigned charge : -0.9999486 assigned positive charge : 909.2159 centred at (gu) : 91.97257 86.59097 87.02071 assigned negative charge : -910.2237 centred at (gu) : 91.40356 86.54721 86.47650 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 231220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52045 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 97698 mr = 166944 m= 20763 mr = 74665 m= 2085 mr = 14211 m= 63 mr = 1148 m= 0 mr = 10 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 3787 time to turn everything in is 1.140000 number of dielectric boundary points 94851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 46699 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) : 1.439605 object centre at (A) : 40.95350 53.42300 37.68350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1300442 0.1774000 midg,1,midg; midg,igrid,midg -1.4961024E-02 -3.0301582E-02 1,midg,midg; igrid,midg,midg -5.7146508E-02 0.1607825 gauss-seidel spectral radius is 0.9991403 estimated iterations to convergence 269 setup time was (sec) 1.370000 now iterating at: 08:49:21 rms-change max change #iterations 10.67410 291.5596 at 10iterations 6.094115 141.7890 at 20iterations 3.464185 70.25844 at 30iterations 1.955251 41.84995 at 40iterations 1.101174 21.79578 at 50iterations 0.6191243 12.89883 at 60iterations 0.3462495 7.898743 at 70iterations 0.1933382 3.773567 at 80iterations 0.1076783 2.222912 at 90iterations 6.0057074E-02 1.282677 at 100iterations 3.3346847E-02 0.7029552 at 110iterations 1.8531533E-02 0.3490810 at 120iterations 1.0281839E-02 0.1892719 at 130iterations 5.7141804E-03 0.1106802 at 140iterations 3.1681794E-03 5.3898811E-02 at 150iterations 1.7564845E-03 3.5509259E-02 at 160iterations 9.7449304E-04 1.7429352E-02 at 170iterations 5.4149056E-04 1.0524750E-02 at 180iterations finished qdiffx linear iterations at : 08:49:33 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 5.4149056E-04 1.0524750E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 08:49:33 13.071u 0.219s 0:13.56 97.9% 0+0k 0+0io 0pf+0w