Tue Nov 22 14:10:45 PST 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 Tue Nov 22 2011 at 14:10:50 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 = 1948 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: 0.5681546 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): -34.50900 12.48700 ymin,ymax (A): 0.3390000 41.60500 zmin,zma (A): -1.467000 61.19200 x,y,z range (A): 46.99600 41.26600 62.65900 scale (grids/A): 0.5681546 object centre (A): -11.01100 20.97200 29.86250 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 285.3841 centred at (gu) : 89.58333 89.73724 88.82005 assigned negative charge : -280.3844 centred at (gu) : 89.47474 89.89722 88.79823 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4244 nv = 96 ne = 84 npr = 39565 no. pairs analyzed = 39565 no. exposed pairs = 2442 no. arc points = 17469 no. surface atoms = 829 nbur = 1119 mkacc time = 8.0000006E-02 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 = 1.540000 m= 200 mr = 2250 m= 0 mr = 22 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1827 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5379 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7846034E-10 7.0231249E-10 midg,1,midg; midg,igrid,midg 2.3202504E-09 -7.4238871E-10 1,midg,midg; igrid,midg,midg -3.3653938E-10 1.5552322E-09 gauss-seidel spectral radius is 0.9839341 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 14:10:53 rms-change max change #iterations 7.0983484E-02 12.70892 at 10iterations 5.3096237E-03 0.9305763 at 20iterations 3.7581101E-04 7.4823380E-02 at 30iterations 2.8004557E-05 5.0492287E-03 at 40iterations 2.1006463E-06 4.3487549E-04 at 50iterations finished qdiffx linear iterations at : 14:10:57 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 2.1006463E-06 4.3487549E-04 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 14:10:59 3.050u 0.153s 0:09.70 32.9% 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 Tue Nov 22 2011 at 14:11:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 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: 1.704464 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): -34.50900 12.48700 ymin,ymax (A): 0.3390000 41.60500 zmin,zma (A): -1.467000 61.19200 x,y,z range (A): 46.99600 41.26600 62.65900 scale (grids/A): 1.704464 object centre (A): -11.01100 20.97200 29.86250 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 285.3841 centred at (gu) : 88.75011 89.21202 86.46045 assigned negative charge : -280.3844 centred at (gu) : 88.42450 89.69185 86.39500 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 46250 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17469 grid for indexing accessible points = 1.400000 m= 15852 mr = 31236 m= 2006 mr = 11668 m= 84 mr = 1181 m= 0 mr = 26 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.3400000 number of dielectric boundary points 20081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 14061 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) : 0.5681546 object centre at (A) : -11.01100 20.97200 29.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1463333E-02 1.6577853E-02 midg,1,midg; midg,igrid,midg 8.9642089E-03 -5.0555402E-03 1,midg,midg; igrid,midg,midg -9.3011116E-04 1.6832027E-03 gauss-seidel spectral radius is 0.9982185 estimated iterations to convergence 188 setup time was (sec) 0.6100000 now iterating at: 14:11:05 rms-change max change #iterations 2.834569 159.8132 at 10iterations 1.186727 57.14285 at 20iterations 0.4984874 22.87135 at 30iterations 0.2094349 9.376245 at 40iterations 8.7795518E-02 4.082130 at 50iterations 3.6856245E-02 1.460869 at 60iterations 1.5475032E-02 0.6762295 at 70iterations 6.5353853E-03 0.2691622 at 80iterations 2.7390844E-03 0.1096692 at 90iterations 1.1508628E-03 4.5799255E-02 at 100iterations 4.8311142E-04 1.8440247E-02 at 110iterations 2.0330356E-04 8.2818866E-03 at 120iterations finished qdiffx linear iterations at : 14:11:25 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 2.0330356E-04 8.2818866E-03 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 14:11:27 7.120u 0.188s 0:26.10 27.9% 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 Tue Nov 22 2011 at 14:11:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 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: 2.556696 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): -34.50900 12.48700 ymin,ymax (A): 0.3390000 41.60500 zmin,zma (A): -1.467000 61.19200 x,y,z range (A): 46.99600 41.26600 62.65900 scale (grids/A): 2.556696 object centre (A): -11.01100 20.97200 29.86250 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 285.3841 centred at (gu) : 88.12519 88.81788 84.69055 assigned negative charge : -280.3844 centred at (gu) : 87.63682 89.53785 84.59258 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 106853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17469 grid for indexing accessible points = 1.400000 m= 52575 mr = 75899 m= 17561 mr = 42885 m= 3542 mr = 14085 m= 425 mr = 2611 m= 13 mr = 272 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 627 time to turn everything in is 0.8000000 number of dielectric boundary points 45217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 14540 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) : 1.704464 object centre at (A) : -11.01100 20.97200 29.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2302569 0.1541805 midg,1,midg; midg,igrid,midg 8.6718775E-02 -7.8144930E-02 1,midg,midg; igrid,midg,midg -2.6863450E-02 2.6276125E-02 gauss-seidel spectral radius is 0.9991134 estimated iterations to convergence 265 setup time was (sec) 1.090000 now iterating at: 14:11:38 rms-change max change #iterations 7.026489 267.0620 at 10iterations 3.873254 112.1546 at 20iterations 2.118101 57.08673 at 30iterations 1.156160 28.59568 at 40iterations 0.6281981 14.90851 at 50iterations 0.3433779 8.503970 at 60iterations 0.1867060 5.029264 at 70iterations 0.1014507 2.574036 at 80iterations 5.5230372E-02 1.749183 at 90iterations 3.0018376E-02 0.6745338 at 100iterations 1.6326219E-02 0.3753700 at 110iterations 8.9074234E-03 0.1999254 at 120iterations 4.8397738E-03 0.1132989 at 130iterations 2.6194246E-03 6.3741684E-02 at 140iterations 1.4264771E-03 3.0994415E-02 at 150iterations 7.7574735E-04 1.7809391E-02 at 160iterations 4.2186989E-04 9.3631744E-03 at 170iterations 2.2897667E-04 5.4491460E-03 at 180iterations finished qdiffx linear iterations at : 14:12:06 total time elapsed so far: 10.33000 # loops : 180 mean,max change (kT/e) : 2.2897667E-04 5.4491460E-03 energy calculations done at 10.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 14:12:08 10.499u 0.160s 0:36.95 28.8% 0+0k 0+0io 0pf+0w