Sun Oct 9 08:57:44 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 08:57:44 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 = 5931 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: 0.4855230 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): 14.91900 80.64700 ymin,ymax (A): 20.53100 85.69600 zmin,zma (A): -5.098000 68.22500 x,y,z range (A): 65.72800 65.16500 73.32300 scale (grids/A): 0.4855230 object centre (A): 47.78300 53.11350 31.56350 number of atom coordinates read : 5931 total number of charged atoms : 5763 net assigned charge : 1.000042 assigned positive charge : 888.5510 centred at (gu) : 90.24133 89.21939 90.85632 assigned negative charge : -887.5590 centred at (gu) : 90.19218 89.25209 91.00764 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8824 nv = 96 ne = 84 npr = 118380 no. pairs analyzed = 118380 no. exposed pairs = 7487 no. arc points = 51428 no. surface atoms = 2505 nbur = 3426 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 = 1.764000 m= 288 mr = 4513 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3900000 number of dielectric boundary points 4598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4896 ## 813 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 11912 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2613803E-10 -1.9819783E-10 midg,1,midg; midg,igrid,midg 4.9189805E-11 -2.3034940E-11 1,midg,midg; igrid,midg,midg -4.3009658E-11 6.0418170E-11 gauss-seidel spectral radius is 0.9783996 estimated iterations to convergence 56 setup time was (sec) 0.5800000 now iterating at: 08:57:45 rms-change max change #iterations 5.8430385E-02 8.654015 at 10iterations 3.2458119E-03 0.5306168 at 20iterations 4.7140589E-04 0.1073971 at 30iterations 1.3139425E-04 3.0878067E-02 at 40iterations 4.0654490E-05 9.2277527E-03 at 50iterations finished qdiffx linear iterations at : 08:57:48 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 4.0654490E-05 9.2277527E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 08:57:48 3.630u 0.179s 0:04.08 93.1% 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 08:57:48 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 = 5931 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: 1.456569 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): 14.91900 80.64700 ymin,ymax (A): 20.53100 85.69600 zmin,zma (A): -5.098000 68.22500 x,y,z range (A): 65.72800 65.16500 73.32300 scale (grids/A): 1.456569 object centre (A): 47.78300 53.11350 31.56350 number of atom coordinates read : 5931 total number of charged atoms : 5763 net assigned charge : 1.000042 assigned positive charge : 888.5510 centred at (gu) : 90.72195 87.65701 92.56707 assigned negative charge : -887.5590 centred at (gu) : 90.57620 87.75605 93.02285 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 101382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 27757 mr = 69632 m= 2091 mr = 17922 m= 34 mr = 793 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1349 time to turn everything in is 0.4800000 number of dielectric boundary points 42915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 845 ## 19 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 42454 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) : 0.4855230 object centre at (A) : 47.78300 53.11350 31.56350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3169683E-02 -3.4622248E-02 midg,1,midg; midg,igrid,midg 2.8637447E-03 -8.5779438E-03 1,midg,midg; igrid,midg,midg 1.8250754E-03 6.1684656E-03 gauss-seidel spectral radius is 0.9979992 estimated iterations to convergence 178 setup time was (sec) 0.7000000 now iterating at: 08:57:49 rms-change max change #iterations 3.845668 175.8167 at 10iterations 1.531902 51.37302 at 20iterations 0.6127854 18.84517 at 30iterations 0.2449418 6.980957 at 40iterations 9.8014683E-02 2.882874 at 50iterations 3.9280426E-02 1.182243 at 60iterations 1.5813034E-02 0.5510483 at 70iterations 6.3785394E-03 0.1972618 at 80iterations 2.5899119E-03 9.9784851E-02 at 90iterations 1.0819394E-03 3.6628723E-02 at 100iterations 4.7241306E-04 1.7456055E-02 at 110iterations 2.2571620E-04 1.0103226E-02 at 120iterations finished qdiffx linear iterations at : 08:57:56 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.2571620E-04 1.0103226E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 08:57:57 7.945u 0.209s 0:08.44 96.4% 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 08:57:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5931 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: 2.184853 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): 14.91900 80.64700 ymin,ymax (A): 20.53100 85.69600 zmin,zma (A): -5.098000 68.22500 x,y,z range (A): 65.72800 65.16500 73.32300 scale (grids/A): 2.184853 object centre (A): 47.78300 53.11350 31.56350 number of atom coordinates read : 5931 total number of charged atoms : 5763 net assigned charge : 1.000042 assigned positive charge : 888.5510 centred at (gu) : 91.08256 86.48499 93.85038 assigned negative charge : -887.5590 centred at (gu) : 90.86421 86.63412 94.53421 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 236091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 102435 mr = 171134 m= 23355 mr = 78779 m= 2714 mr = 16355 m= 99 mr = 1516 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 4716 time to turn everything in is 1.160000 number of dielectric boundary points 96885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 45880 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) : 1.456569 object centre at (A) : 47.78300 53.11350 31.56350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5453320 -0.9634021 midg,1,midg; midg,igrid,midg 0.1028810 -0.1813804 1,midg,midg; igrid,midg,midg 4.0823705E-02 8.0320105E-02 gauss-seidel spectral radius is 0.9991623 estimated iterations to convergence 273 setup time was (sec) 1.400000 now iterating at: 08:57:58 rms-change max change #iterations 10.77688 302.4812 at 10iterations 6.203182 143.5931 at 20iterations 3.554804 80.22176 at 30iterations 2.023148 45.96317 at 40iterations 1.150365 22.81713 at 50iterations 0.6487817 13.61481 at 60iterations 0.3671041 8.029909 at 70iterations 0.2063825 4.698204 at 80iterations 0.1160646 2.594367 at 90iterations 6.4996988E-02 1.216231 at 100iterations 3.6436979E-02 0.6937990 at 110iterations 2.0433735E-02 0.3729849 at 120iterations 1.1447099E-02 0.2023239 at 130iterations 6.4032967E-03 0.1135502 at 140iterations 3.5870285E-03 6.3217163E-02 at 150iterations 2.0175562E-03 3.7414551E-02 at 160iterations 1.1383002E-03 2.3138165E-02 at 170iterations 6.5023231E-04 1.2067795E-02 at 180iterations finished qdiffx linear iterations at : 08:58:10 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 6.5023231E-04 1.2067795E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 08:58:10 13.094u 0.217s 0:13.66 97.3% 0+0k 0+0io 0pf+0w