Sun Oct 9 08:12:59 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 Sun Oct 9 2011 at 08:12:59 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 !!! WARNING: NAP 529 has a net charge of -2.0000 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: 0.5352257 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): 23.41400 89.92800 ymin,ymax (A): -47.80300 5.305000 zmin,zma (A): 19.80300 68.97200 x,y,z range (A): 66.51400 53.10800 49.16900 scale (grids/A): 0.5352257 object centre (A): 56.67100 -21.24900 44.38750 number of atom coordinates read : 3151 total number of charged atoms : 3013 net assigned charge : 9.000031 assigned positive charge : 473.5191 centred at (gu) : 89.33768 89.39925 89.46365 assigned negative charge : -464.5202 centred at (gu) : 89.25636 89.38684 89.47577 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5880 nv = 96 ne = 84 npr = 63681 no. pairs analyzed = 63681 no. exposed pairs = 3869 no. arc points = 27665 no. surface atoms = 1295 nbur = 1856 mkacc time = 0.1000000 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 = 1.596000 m= 207 mr = 3055 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.2100000 number of dielectric boundary points 3021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2742 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8324383E-10 2.7374869E-10 midg,1,midg; midg,igrid,midg 3.5922570E-10 3.6635586E-10 1,midg,midg; igrid,midg,midg -1.6210953E-11 6.2562550E-10 gauss-seidel spectral radius is 0.9820242 estimated iterations to convergence 61 setup time was (sec) 0.4000000 now iterating at: 08:13:00 rms-change max change #iterations 6.9145277E-02 12.08197 at 10iterations 4.4312482E-03 0.7983027 at 20iterations 3.2565973E-04 4.5232773E-02 at 30iterations 4.3362965E-05 6.0043335E-03 at 40iterations 9.8082419E-06 1.3960600E-03 at 50iterations finished qdiffx linear iterations at : 08:13:02 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 9.8082419E-06 1.3960600E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 08:13:03 3.395u 0.180s 0:03.86 92.4% 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 08:13:03 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 !!! WARNING: NAP 529 has a net charge of -2.0000 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: 1.605677 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): 23.41400 89.92800 ymin,ymax (A): -47.80300 5.305000 zmin,zma (A): 19.80300 68.97200 x,y,z range (A): 66.51400 53.10800 49.16900 scale (grids/A): 1.605677 object centre (A): 56.67100 -21.24900 44.38750 number of atom coordinates read : 3151 total number of charged atoms : 3013 net assigned charge : 9.000031 assigned positive charge : 473.5191 centred at (gu) : 88.01257 88.19707 88.39038 assigned negative charge : -464.5202 centred at (gu) : 87.76882 88.16028 88.42704 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27665 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19759 mr = 45109 m= 1982 mr = 13454 m= 59 mr = 938 m= 0 mr = 7 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 3196 time to turn everything in is 0.3300000 number of dielectric boundary points 27958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 23024 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) : 0.5352257 object centre at (A) : 56.67100 -21.24900 44.38750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4344979E-03 1.4782198E-03 midg,1,midg; midg,igrid,midg 8.0704261E-03 7.8073246E-03 1,midg,midg; igrid,midg,midg -1.0178433E-03 1.3218931E-02 gauss-seidel spectral radius is 0.9981423 estimated iterations to convergence 184 setup time was (sec) 0.5500000 now iterating at: 08:13:04 rms-change max change #iterations 3.295746 140.0329 at 10iterations 1.358361 50.43655 at 20iterations 0.5621044 22.06168 at 30iterations 0.2313914 8.695278 at 40iterations 9.5926642E-02 3.360139 at 50iterations 3.9620828E-02 1.439337 at 60iterations 1.6305361E-02 0.6387730 at 70iterations 6.7472681E-03 0.2407084 at 80iterations 2.8008407E-03 9.9868774E-02 at 90iterations 1.1632040E-03 4.0004253E-02 at 100iterations 4.8313473E-04 1.6422272E-02 at 110iterations 2.0138235E-04 7.1096420E-03 at 120iterations finished qdiffx linear iterations at : 08:13:11 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.0138235E-04 7.1096420E-03 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:13:11 7.616u 0.192s 0:08.10 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 Sun Oct 9 2011 at 08:13:11 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 !!! WARNING: NAP 529 has a net charge of -2.0000 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: 2.408515 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): 23.41400 89.92800 ymin,ymax (A): -47.80300 5.305000 zmin,zma (A): 19.80300 68.97200 x,y,z range (A): 66.51400 53.10800 49.16900 scale (grids/A): 2.408515 object centre (A): 56.67100 -21.24900 44.38750 number of atom coordinates read : 3151 total number of charged atoms : 3013 net assigned charge : 9.000031 assigned positive charge : 473.5191 centred at (gu) : 87.01873 87.29544 87.58528 assigned negative charge : -464.5202 centred at (gu) : 86.65310 87.24025 87.64056 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152971 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27665 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 69153 mr = 110606 m= 19266 mr = 54580 m= 2980 mr = 14355 m= 206 mr = 1835 m= 4 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 11204 time to turn everything in is 0.7700000 number of dielectric boundary points 63113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 24059 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) : 1.605677 object centre at (A) : 56.67100 -21.24900 44.38750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1581010 2.5833782E-02 midg,1,midg; midg,igrid,midg 0.1140600 0.1104201 1,midg,midg; igrid,midg,midg -0.1613111 0.2514048 gauss-seidel spectral radius is 0.9991303 estimated iterations to convergence 268 setup time was (sec) 1.000000 now iterating at: 08:13:12 rms-change max change #iterations 8.661291 264.4966 at 10iterations 4.907226 159.2609 at 20iterations 2.755528 73.22130 at 30iterations 1.538711 41.38195 at 40iterations 0.8531340 19.87490 at 50iterations 0.4729643 11.62083 at 60iterations 0.2613153 6.175403 at 70iterations 0.1443475 3.568722 at 80iterations 7.9575948E-02 1.645392 at 90iterations 4.3814868E-02 0.9143181 at 100iterations 2.4121821E-02 0.5161586 at 110iterations 1.3274129E-02 0.2895832 at 120iterations 7.2881575E-03 0.1779022 at 130iterations 4.0094866E-03 8.8136673E-02 at 140iterations 2.1979704E-03 4.9377441E-02 at 150iterations 1.2047186E-03 2.6309907E-02 at 160iterations 6.6116359E-04 1.4133453E-02 at 170iterations 3.6268795E-04 7.4024200E-03 at 180iterations finished qdiffx linear iterations at : 08:13:23 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 3.6268795E-04 7.4024200E-03 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 08:13:24 12.051u 0.210s 0:12.53 97.8% 0+0k 0+0io 0pf+0w