Mon Oct 10 11:50:16 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 Mon Oct 10 2011 at 11:50:16 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: GLU 207 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: 0.5785890 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): -2.911000 42.25800 ymin,ymax (A): 19.86800 67.16400 zmin,zma (A): -22.87900 38.65000 x,y,z range (A): 45.16900 47.29600 61.52900 scale (grids/A): 0.5785890 object centre (A): 19.67350 43.51600 7.885501 number of atom coordinates read : 2153 total number of charged atoms : 2015 net assigned charge : -6.999990 assigned positive charge : 323.1119 centred at (gu) : 90.77889 89.84048 88.32749 assigned negative charge : -330.1119 centred at (gu) : 90.69324 89.82808 88.35085 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4495 nv = 96 ne = 84 npr = 45126 no. pairs analyzed = 45126 no. exposed pairs = 2695 no. arc points = 19074 no. surface atoms = 911 nbur = 1242 mkacc time = 0.1200000 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 = 1.484000 m= 196 mr = 2276 m= 0 mr = 6 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2700000 number of dielectric boundary points 2409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 5843 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6133281E-09 -1.2528687E-09 midg,1,midg; midg,igrid,midg -1.7231383E-09 -1.2307840E-09 1,midg,midg; igrid,midg,midg -2.3487967E-09 -1.6510066E-10 gauss-seidel spectral radius is 0.9845109 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 11:50:43 rms-change max change #iterations 7.9870746E-02 15.04609 at 10iterations 6.1527127E-03 1.279072 at 20iterations 4.7714068E-04 8.6039543E-02 at 30iterations 3.6790596E-05 6.2713623E-03 at 40iterations 2.8059280E-06 4.9877167E-04 at 50iterations finished qdiffx linear iterations at : 11:50:48 total time elapsed so far: 5.050000 # loops : 50 mean,max change (kT/e) : 2.8059280E-06 4.9877167E-04 energy calculations done at 5.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.220000 DelPhi exited at 11:50:48 5.222u 0.531s 0:32.58 17.6% 0+0k 0+0io 6pf+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 11:50:48 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: GLU 207 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: 1.735767 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): -2.911000 42.25800 ymin,ymax (A): 19.86800 67.16400 zmin,zma (A): -22.87900 38.65000 x,y,z range (A): 45.16900 47.29600 61.52900 scale (grids/A): 1.735767 object centre (A): 19.67350 43.51600 7.885501 number of atom coordinates read : 2153 total number of charged atoms : 2015 net assigned charge : -6.999990 assigned positive charge : 323.1119 centred at (gu) : 92.33632 89.52122 84.98225 assigned negative charge : -330.1119 centred at (gu) : 92.07955 89.48411 85.05257 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 49475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19074 grid for indexing accessible points = 1.400000 m= 15323 mr = 32654 m= 1734 mr = 10568 m= 52 mr = 927 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1060 time to turn everything in is 0.4300000 number of dielectric boundary points 22429 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 15604 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) : 0.5785890 object centre at (A) : 19.67350 43.51600 7.885501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2838288E-03 -2.8467309E-03 midg,1,midg; midg,igrid,midg -4.3636868E-03 -1.1243820E-02 1,midg,midg; igrid,midg,midg -1.0464109E-02 1.4779201E-03 gauss-seidel spectral radius is 0.9982999 estimated iterations to convergence 193 setup time was (sec) 0.7600000 now iterating at: 11:51:02 rms-change max change #iterations 3.161514 186.5993 at 10iterations 1.351326 60.75519 at 20iterations 0.5776042 24.42842 at 30iterations 0.2476550 10.08032 at 40iterations 0.1059660 4.467593 at 50iterations 4.5254543E-02 1.828762 at 60iterations 1.9484574E-02 0.7515869 at 70iterations 8.3365049E-03 0.3543401 at 80iterations 3.5753720E-03 0.1617751 at 90iterations 1.5297418E-03 5.6568146E-02 at 100iterations 6.5353769E-04 2.5357246E-02 at 110iterations 2.8073779E-04 1.0927200E-02 at 120iterations finished qdiffx linear iterations at : 11:51:13 total time elapsed so far: 11.45000 # loops : 120 mean,max change (kT/e) : 2.8073779E-04 1.0927200E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 11:51:14 11.613u 0.551s 0:25.41 47.8% 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 11:51:14 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: GLU 207 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: 2.603650 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): -2.911000 42.25800 ymin,ymax (A): 19.86800 67.16400 zmin,zma (A): -22.87900 38.65000 x,y,z range (A): 45.16900 47.29600 61.52900 scale (grids/A): 2.603650 object centre (A): 19.67350 43.51600 7.885501 number of atom coordinates read : 2153 total number of charged atoms : 2015 net assigned charge : -6.999990 assigned positive charge : 323.1119 centred at (gu) : 93.50446 89.28188 82.47332 assigned negative charge : -330.1119 centred at (gu) : 93.11926 89.22611 82.57883 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 114531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19074 grid for indexing accessible points = 1.400000 m= 52058 mr = 79653 m= 15455 mr = 41105 m= 2845 mr = 11652 m= 251 mr = 2010 m= 3 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 3578 time to turn everything in is 1.040000 number of dielectric boundary points 50604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 16111 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) : 1.735767 object centre at (A) : 19.67350 43.51600 7.885501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5634818E-02 1.5823239E-02 midg,1,midg; midg,igrid,midg -2.2157451E-02 -0.1307784 1,midg,midg; igrid,midg,midg -0.1410928 4.3582674E-02 gauss-seidel spectral radius is 0.9991454 estimated iterations to convergence 270 setup time was (sec) 1.400000 now iterating at: 11:51:16 rms-change max change #iterations 7.829736 283.9369 at 10iterations 4.360669 109.2436 at 20iterations 2.413210 75.21555 at 30iterations 1.330321 28.46064 at 40iterations 0.7329557 17.94066 at 50iterations 0.4028554 8.735382 at 60iterations 0.2215777 5.059846 at 70iterations 0.1218395 2.719296 at 80iterations 6.7093655E-02 1.574697 at 90iterations 3.6901843E-02 0.9407902 at 100iterations 2.0279575E-02 0.4967537 at 110iterations 1.1149961E-02 0.2743835 at 120iterations 6.1212243E-03 0.1391802 at 130iterations 3.3680326E-03 7.7033997E-02 at 140iterations 1.8478096E-03 4.3731689E-02 at 150iterations 1.0162055E-03 2.5012970E-02 at 160iterations 5.5969460E-04 1.2598038E-02 at 170iterations 3.0772435E-04 7.6293945E-03 at 180iterations finished qdiffx linear iterations at : 11:51:33 total time elapsed so far: 18.41000 # loops : 180 mean,max change (kT/e) : 3.0772435E-04 7.6293945E-03 energy calculations done at 18.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.56000 DelPhi exited at 11:51:34 18.569u 0.551s 0:19.84 96.3% 0+0k 0+0io 0pf+0w