Sun Oct 9 10:40:32 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 10:40:32 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 = 2822 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6167599 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): -69.95900 -18.53700 ymin,ymax (A): 7.919000 61.96100 zmin,zma (A): -30.06000 27.66100 x,y,z range (A): 51.42200 54.04200 57.72100 scale (grids/A): 0.6167599 object centre (A): -44.24800 34.94000 -1.199500 number of atom coordinates read : 2822 total number of charged atoms : 2679 net assigned charge : -0.4999826 assigned positive charge : 412.4921 centred at (gu) : 90.00172 92.03081 90.95459 assigned negative charge : -412.9937 centred at (gu) : 90.07254 92.02216 90.97266 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7518 nv = 96 ne = 84 npr = 55162 no. pairs analyzed = 55162 no. exposed pairs = 3970 no. arc points = 28333 no. surface atoms = 1313 nbur = 1509 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 3804 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2748 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3628791E-10 -1.8828989E-09 midg,1,midg; midg,igrid,midg -5.8809202E-10 3.1843927E-10 1,midg,midg; igrid,midg,midg 4.1327444E-09 -4.9322377E-09 gauss-seidel spectral radius is 0.9864260 estimated iterations to convergence 70 setup time was (sec) 0.5700000 now iterating at: 10:40:33 rms-change max change #iterations 0.1255281 19.35210 at 10iterations 1.1155925E-02 1.719568 at 20iterations 1.0308040E-03 0.1632652 at 30iterations 1.1811937E-04 1.8054962E-02 at 40iterations 2.5385758E-05 4.4710636E-03 at 50iterations finished qdiffx linear iterations at : 10:40:36 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.5385758E-05 4.4710636E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 10:40:36 3.393u 0.181s 0:03.89 91.7% 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 10:40:36 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 = 2822 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.850280 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): -69.95900 -18.53700 ymin,ymax (A): 7.919000 61.96100 zmin,zma (A): -30.06000 27.66100 x,y,z range (A): 51.42200 54.04200 57.72100 scale (grids/A): 1.850280 object centre (A): -44.24800 34.94000 -1.199500 number of atom coordinates read : 2822 total number of charged atoms : 2679 net assigned charge : -0.4999826 assigned positive charge : 412.4921 centred at (gu) : 90.00453 96.09151 92.86282 assigned negative charge : -412.9937 centred at (gu) : 90.21764 96.06630 92.91782 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28333 grid for indexing accessible points = 1.400000 m= 28614 mr = 53767 m= 4488 mr = 20085 m= 232 mr = 2591 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 38071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21003 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) : 0.6167599 object centre at (A) : -44.24800 34.94000 -1.199500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5450176E-02 -6.9090244E-03 midg,1,midg; midg,igrid,midg -1.2941671E-02 -1.1033761E-02 1,midg,midg; igrid,midg,midg 1.6458852E-02 -2.8912589E-02 gauss-seidel spectral radius is 0.9986090 estimated iterations to convergence 213 setup time was (sec) 0.8700000 now iterating at: 10:40:37 rms-change max change #iterations 4.176472 193.9923 at 10iterations 1.941270 67.98803 at 20iterations 0.9026898 28.90123 at 30iterations 0.4183259 12.63914 at 40iterations 0.1944494 6.468596 at 50iterations 9.0664923E-02 2.982601 at 60iterations 4.2122200E-02 1.386627 at 70iterations 1.9523742E-02 0.6703112 at 80iterations 9.1248322E-03 0.2940645 at 90iterations 4.2343372E-03 0.1225797 at 100iterations 1.9766691E-03 6.3400269E-02 at 110iterations 9.2432601E-04 2.9323578E-02 at 120iterations finished qdiffx linear iterations at : 10:40:44 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 9.2432601E-04 2.9323578E-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) 7.740000 DelPhi exited at 10:40:45 7.745u 0.212s 0:08.36 95.0% 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 10:40:45 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 = 2822 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.775420 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): -69.95900 -18.53700 ymin,ymax (A): 7.919000 61.96100 zmin,zma (A): -30.06000 27.66100 x,y,z range (A): 51.42200 54.04200 57.72100 scale (grids/A): 2.775420 object centre (A): -44.24800 34.94000 -1.199500 number of atom coordinates read : 2822 total number of charged atoms : 2679 net assigned charge : -0.4999826 assigned positive charge : 412.4921 centred at (gu) : 90.00668 99.13707 94.29393 assigned negative charge : -412.9937 centred at (gu) : 90.32642 99.09943 94.37682 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 187931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28333 grid for indexing accessible points = 1.400000 m= 91675 mr = 131416 m= 33085 mr = 72354 m= 7965 mr = 25790 m= 1051 mr = 5680 m= 45 mr = 656 m= 0 mr = 22 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 85834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 21429 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) : 1.850280 object centre at (A) : -44.24800 34.94000 -1.199500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3384301 -5.5543404E-02 midg,1,midg; midg,igrid,midg -0.1518334 -9.1139317E-02 1,midg,midg; igrid,midg,midg 0.2342850 -0.4113078 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.800000 now iterating at: 10:40:47 rms-change max change #iterations 10.13558 324.3716 at 10iterations 6.062953 147.2988 at 20iterations 3.588793 79.69888 at 30iterations 2.110828 43.88613 at 40iterations 1.237932 26.94220 at 50iterations 0.7234814 13.92830 at 60iterations 0.4232638 8.500263 at 70iterations 0.2460204 4.682140 at 80iterations 0.1431043 2.765398 at 90iterations 8.3011732E-02 1.530971 at 100iterations 4.8223391E-02 0.8781176 at 110iterations 2.7997708E-02 0.6072502 at 120iterations 1.6217146E-02 0.2922611 at 130iterations 9.3811294E-03 0.1660714 at 140iterations 5.4300525E-03 9.7714484E-02 at 150iterations 3.1480419E-03 6.1647415E-02 at 160iterations 1.8203892E-03 3.3294678E-02 at 170iterations 1.0529906E-03 1.7606735E-02 at 180iterations finished qdiffx linear iterations at : 10:40:58 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.0529906E-03 1.7606735E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 10:40:58 13.091u 0.212s 0:13.65 97.4% 0+0k 0+0io 0pf+0w