Mon Oct 10 17:02:31 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 Mon Oct 10 2011 at 17:02:31 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6223558 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): -8.657001 48.54500 ymin,ymax (A): -8.356000 39.19100 zmin,zma (A): -0.3809999 55.21300 x,y,z range (A): 57.20200 47.54700 55.59400 scale (grids/A): 0.6223558 object centre (A): 19.94400 15.41750 27.41600 number of atom coordinates read : 2791 total number of charged atoms : 2650 net assigned charge : -3.485977 assigned positive charge : 422.4412 centred at (gu) : 88.94310 89.38818 89.14196 assigned negative charge : -425.9283 centred at (gu) : 88.84666 89.29189 89.09407 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7243 nv = 96 ne = 84 npr = 55678 no. pairs analyzed = 55678 no. exposed pairs = 3725 no. arc points = 26211 no. surface atoms = 1255 nbur = 1536 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3745 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3800000 number of dielectric boundary points 3833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2551 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8853 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9376985E-09 7.0763373E-10 midg,1,midg; midg,igrid,midg -1.1915181E-08 3.9920360E-09 1,midg,midg; igrid,midg,midg -1.3172785E-08 3.6143886E-09 gauss-seidel spectral radius is 0.9866532 estimated iterations to convergence 71 setup time was (sec) 0.6600000 now iterating at: 17:02:32 rms-change max change #iterations 0.1326047 23.33846 at 10iterations 1.2258211E-02 1.690580 at 20iterations 1.1444021E-03 0.1546783 at 30iterations 1.0383152E-04 1.5123129E-02 at 40iterations 9.8250730E-06 1.3465881E-03 at 50iterations finished qdiffx linear iterations at : 17:02:35 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 9.8250730E-06 1.3465881E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 17:02:36 4.170u 0.251s 0:05.65 78.2% 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 Mon Oct 10 2011 at 17:02:36 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.867067 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): -8.657001 48.54500 ymin,ymax (A): -8.356000 39.19100 zmin,zma (A): -0.3809999 55.21300 x,y,z range (A): 57.20200 47.54700 55.59400 scale (grids/A): 1.867067 object centre (A): 19.94400 15.41750 27.41600 number of atom coordinates read : 2791 total number of charged atoms : 2650 net assigned charge : -3.485977 assigned positive charge : 422.4412 centred at (gu) : 86.82861 88.16412 87.42504 assigned negative charge : -425.9283 centred at (gu) : 86.53976 87.87566 87.28172 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26211 grid for indexing accessible points = 1.400000 m= 26036 mr = 52642 m= 3546 mr = 18335 m= 150 mr = 1989 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1198 time to turn everything in is 0.6900000 number of dielectric boundary points 35434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20780 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) : 0.6223558 object centre at (A) : 19.94400 15.41750 27.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6732812E-03 1.3248259E-04 midg,1,midg; midg,igrid,midg -1.6692121E-02 -3.2649648E-03 1,midg,midg; igrid,midg,midg -5.6421008E-02 2.8168878E-02 gauss-seidel spectral radius is 0.9986106 estimated iterations to convergence 213 setup time was (sec) 0.9900000 now iterating at: 17:02:38 rms-change max change #iterations 4.281417 188.4782 at 10iterations 1.986966 74.81557 at 20iterations 0.9231981 31.79752 at 30iterations 0.4276864 14.42084 at 40iterations 0.1987330 6.098724 at 50iterations 9.2184104E-02 2.759937 at 60iterations 4.2938255E-02 1.311493 at 70iterations 1.9911528E-02 0.6232419 at 80iterations 9.2270644E-03 0.2992430 at 90iterations 4.3130778E-03 0.1423340 at 100iterations 2.0009789E-03 6.5743446E-02 at 110iterations 9.2764094E-04 2.8259277E-02 at 120iterations finished qdiffx linear iterations at : 17:02:46 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 9.2764094E-04 2.8259277E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 17:02:47 9.520u 0.289s 0:10.20 96.0% 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 Mon Oct 10 2011 at 17:02:47 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.800601 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): -8.657001 48.54500 ymin,ymax (A): -8.356000 39.19100 zmin,zma (A): -0.3809999 55.21300 x,y,z range (A): 57.20200 47.54700 55.59400 scale (grids/A): 2.800601 object centre (A): 19.94400 15.41750 27.41600 number of atom coordinates read : 2791 total number of charged atoms : 2650 net assigned charge : -3.485977 assigned positive charge : 422.4412 centred at (gu) : 85.24257 87.24592 86.13745 assigned negative charge : -425.9283 centred at (gu) : 84.80947 86.81345 85.92262 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 182363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26211 grid for indexing accessible points = 1.400000 m= 86116 mr = 128698 m= 28732 mr = 68487 m= 6073 mr = 22304 m= 658 mr = 4259 m= 25 mr = 373 m= 0 mr = 14 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 3966 time to turn everything in is 1.760000 number of dielectric boundary points 79832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 21200 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) : 1.867067 object centre at (A) : 19.94400 15.41750 27.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1779853 -0.2632549 midg,1,midg; midg,igrid,midg -0.1156284 -7.2655298E-02 1,midg,midg; igrid,midg,midg -0.6507540 0.3864880 gauss-seidel spectral radius is 0.9992754 estimated iterations to convergence 293 setup time was (sec) 2.100000 now iterating at: 17:02:49 rms-change max change #iterations 10.35352 327.6323 at 10iterations 6.168218 176.8620 at 20iterations 3.641846 82.16310 at 30iterations 2.134364 49.47683 at 40iterations 1.247304 26.48247 at 50iterations 0.7266324 14.34764 at 60iterations 0.4223237 7.633425 at 70iterations 0.2457857 4.488509 at 80iterations 0.1424785 2.602596 at 90iterations 8.2414776E-02 1.705661 at 100iterations 4.7852479E-02 0.9337921 at 110iterations 2.7651750E-02 0.4803505 at 120iterations 1.6018081E-02 0.3031082 at 130iterations 9.2607709E-03 0.1673279 at 140iterations 5.3499578E-03 0.1139703 at 150iterations 3.0991449E-03 5.5341244E-02 at 160iterations 1.7943283E-03 3.2300472E-02 at 170iterations 1.0398269E-03 1.9071579E-02 at 180iterations finished qdiffx linear iterations at : 17:03:03 total time elapsed so far: 15.86000 # loops : 180 mean,max change (kT/e) : 1.0398269E-03 1.9071579E-02 energy calculations done at 15.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 17:03:04 16.032u 0.292s 0:17.60 92.7% 0+0k 0+0io 0pf+0w