Sun Oct 9 07:12:57 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 07:12:57 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6576273 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): -13.18200 38.45000 ymin,ymax (A): -22.31700 29.58800 zmin,zma (A): -15.41800 38.71600 x,y,z range (A): 51.63200 51.90500 54.13400 scale (grids/A): 0.6576273 object centre (A): 12.63400 3.635500 11.64900 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 90.56505 90.29812 89.36202 assigned negative charge : -298.1052 centred at (gu) : 90.71832 90.21002 89.21867 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5809 nv = 96 ne = 84 npr = 41740 no. pairs analyzed = 41740 no. exposed pairs = 2450 no. arc points = 17671 no. surface atoms = 834 nbur = 1170 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3125 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.1700000 number of dielectric boundary points 2962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1702 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0806565E-08 1.9965540E-08 midg,1,midg; midg,igrid,midg -9.4132684E-09 1.6123279E-08 1,midg,midg; igrid,midg,midg 2.1491708E-08 -2.2131205E-08 gauss-seidel spectral radius is 0.9879633 estimated iterations to convergence 74 setup time was (sec) 0.3600000 now iterating at: 07:12:57 rms-change max change #iterations 0.1443697 24.13992 at 10iterations 1.5345095E-02 2.506547 at 20iterations 1.6507973E-03 0.2610283 at 30iterations 1.6975551E-04 3.1420708E-02 at 40iterations 1.7574972E-05 2.7084351E-03 at 50iterations finished qdiffx linear iterations at : 07:13:00 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.7574972E-05 2.7084351E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:13:01 3.324u 0.157s 0:03.74 92.7% 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 07:13:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.972882 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): -13.18200 38.45000 ymin,ymax (A): -22.31700 29.58800 zmin,zma (A): -15.41800 38.71600 x,y,z range (A): 51.63200 51.90500 54.13400 scale (grids/A): 1.972882 object centre (A): 12.63400 3.635500 11.64900 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 91.69536 90.89444 88.08594 assigned negative charge : -298.1052 centred at (gu) : 92.15519 90.63001 87.65592 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17671 grid for indexing accessible points = 1.400000 m= 22493 mr = 42195 m= 3575 mr = 16724 m= 241 mr = 2278 m= 3 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 438 time to turn everything in is 0.3200000 number of dielectric boundary points 27093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14739 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) : 0.6576273 object centre at (A) : 12.63400 3.635500 11.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0415944E-02 1.4848514E-02 midg,1,midg; midg,igrid,midg 1.3335872E-02 3.8908295E-02 1,midg,midg; igrid,midg,midg 1.0529531E-02 -3.5723280E-02 gauss-seidel spectral radius is 0.9986673 estimated iterations to convergence 217 setup time was (sec) 0.5400000 now iterating at: 07:13:01 rms-change max change #iterations 3.958608 180.7996 at 10iterations 1.880356 77.74221 at 20iterations 0.8850547 31.87082 at 30iterations 0.4193588 13.68476 at 40iterations 0.1965682 6.898932 at 50iterations 9.3208976E-02 3.048145 at 60iterations 4.4068258E-02 1.522832 at 70iterations 2.0893216E-02 0.7196522 at 80iterations 9.8435013E-03 0.3461461 at 90iterations 4.6573826E-03 0.1510086 at 100iterations 2.1864404E-03 7.3392868E-02 at 110iterations 1.0362425E-03 3.3287048E-02 at 120iterations finished qdiffx linear iterations at : 07:13:09 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.0362425E-03 3.3287048E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 07:13:09 7.801u 0.227s 0:08.35 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 Sun Oct 9 2011 at 07:13:09 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.959323 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): -13.18200 38.45000 ymin,ymax (A): -22.31700 29.58800 zmin,zma (A): -15.41800 38.71600 x,y,z range (A): 51.63200 51.90500 54.13400 scale (grids/A): 2.959323 object centre (A): 12.63400 3.635500 11.64900 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 92.54307 91.34179 87.12890 assigned negative charge : -298.1052 centred at (gu) : 93.23285 90.94502 86.48387 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 142948 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17671 grid for indexing accessible points = 1.400000 m= 72559 mr = 101995 m= 26625 mr = 59637 m= 6416 mr = 21434 m= 1029 mr = 4819 m= 117 mr = 746 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 1558 time to turn everything in is 0.8300000 number of dielectric boundary points 60988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14935 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) : 1.972882 object centre at (A) : 12.63400 3.635500 11.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6078188 9.8615259E-02 midg,1,midg; midg,igrid,midg 0.1829091 0.4083136 1,midg,midg; igrid,midg,midg 0.1646860 -0.2913699 gauss-seidel spectral radius is 0.9992571 estimated iterations to convergence 290 setup time was (sec) 1.050000 now iterating at: 07:13:10 rms-change max change #iterations 9.092586 460.5990 at 10iterations 5.240583 135.6090 at 20iterations 3.015511 63.03161 at 30iterations 1.732646 35.18298 at 40iterations 0.9933392 19.44629 at 50iterations 0.5696307 12.08350 at 60iterations 0.3268219 6.038651 at 70iterations 0.1873089 3.482815 at 80iterations 0.1075401 2.268797 at 90iterations 6.1422836E-02 1.180130 at 100iterations 3.5221681E-02 0.7362537 at 110iterations 2.0174470E-02 0.4223757 at 120iterations 1.1563330E-02 0.2292066 at 130iterations 6.6406960E-03 0.1288768 at 140iterations 3.7956417E-03 7.2033405E-02 at 150iterations 2.1784729E-03 4.0927052E-02 at 160iterations 1.2459715E-03 2.2823334E-02 at 170iterations 7.1504613E-04 1.4209747E-02 at 180iterations finished qdiffx linear iterations at : 07:13:22 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 7.1504613E-04 1.4209747E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 07:13:22 12.346u 0.220s 0:12.82 97.9% 0+0k 0+0io 0pf+0w