Tue Oct 11 05:24:06 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 Tue Oct 11 2011 at 05:24:06 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 = 2234 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6961691 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): 19.84000 63.23300 ymin,ymax (A): -3.477000 33.56600 zmin,zma (A): 20.10700 71.24400 x,y,z range (A): 43.39300 37.04300 51.13700 scale (grids/A): 0.6961691 object centre (A): 41.53650 15.04450 45.67550 number of atom coordinates read : 2234 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.9671 centred at (gu) : 90.17823 89.67978 89.60469 assigned negative charge : -304.9422 centred at (gu) : 90.35546 89.70016 89.58125 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6800 nv = 96 ne = 84 npr = 40576 no. pairs analyzed = 40576 no. exposed pairs = 2522 no. arc points = 17067 no. surface atoms = 867 nbur = 1367 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 3903 m= 5 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1674 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9469853E-08 5.0221118E-08 midg,1,midg; midg,igrid,midg 5.6426078E-08 3.5579141E-08 1,midg,midg; igrid,midg,midg 1.0678409E-07 -2.3043132E-08 gauss-seidel spectral radius is 0.9892446 estimated iterations to convergence 79 setup time was (sec) 0.6300000 now iterating at: 05:24:07 rms-change max change #iterations 0.1852404 26.44386 at 10iterations 2.2250934E-02 3.201261 at 20iterations 2.9072766E-03 0.4130173 at 30iterations 5.0342805E-04 6.2723160E-02 at 40iterations 1.3321628E-04 1.8314362E-02 at 50iterations finished qdiffx linear iterations at : 05:24:10 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 1.3321628E-04 1.8314362E-02 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 05:24:11 4.270u 0.235s 0:04.98 90.3% 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 Oct 11 2011 at 05:24:11 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.088507 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): 19.84000 63.23300 ymin,ymax (A): -3.477000 33.56600 zmin,zma (A): 20.10700 71.24400 x,y,z range (A): 43.39300 37.04300 51.13700 scale (grids/A): 2.088507 object centre (A): 41.53650 15.04450 45.67550 number of atom coordinates read : 2234 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.9671 centred at (gu) : 90.53460 89.03957 88.81424 assigned negative charge : -304.9422 centred at (gu) : 91.06648 89.10069 88.74384 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 72000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17067 grid for indexing accessible points = 1.400000 m= 29283 mr = 51164 m= 5723 mr = 22355 m= 503 mr = 3835 m= 13 mr = 253 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 29915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 15294 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) : 0.6961691 object centre at (A) : 41.53650 15.04450 45.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5897614E-02 3.9910834E-02 midg,1,midg; midg,igrid,midg 2.4263211E-02 1.0579232E-02 1,midg,midg; igrid,midg,midg 3.9569333E-02 8.9371242E-03 gauss-seidel spectral radius is 0.9987955 estimated iterations to convergence 228 setup time was (sec) 1.110000 now iterating at: 05:24:12 rms-change max change #iterations 4.442342 202.8004 at 10iterations 2.185273 81.63096 at 20iterations 1.067744 32.09812 at 30iterations 0.5271699 18.47349 at 40iterations 0.2592844 8.857317 at 50iterations 0.1274917 4.205992 at 60iterations 6.2667720E-02 2.043709 at 70iterations 3.0898150E-02 0.9671776 at 80iterations 1.5334642E-02 0.4554729 at 90iterations 7.6625408E-03 0.2225342 at 100iterations 3.8520412E-03 0.1231003 at 110iterations 1.9979519E-03 6.5830231E-02 at 120iterations finished qdiffx linear iterations at : 05:24:21 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 1.9979519E-03 6.5830231E-02 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 05:24:22 9.804u 0.255s 0:10.59 94.9% 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 Oct 11 2011 at 05:24:22 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 = 2234 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.132761 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): 19.84000 63.23300 ymin,ymax (A): -3.477000 33.56600 zmin,zma (A): 20.10700 71.24400 x,y,z range (A): 43.39300 37.04300 51.13700 scale (grids/A): 3.132761 object centre (A): 41.53650 15.04450 45.67550 number of atom coordinates read : 2234 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.9671 centred at (gu) : 90.80178 88.55936 88.22135 assigned negative charge : -304.9422 centred at (gu) : 91.59975 88.65112 88.11582 start vw surface at 0.1800000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 165869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17067 grid for indexing accessible points = 1.400000 m= 91027 mr = 123035 m= 37360 mr = 75933 m= 10717 mr = 30744 m= 2076 mr = 8393 m= 209 mr = 1549 m= 3 mr = 123 m= 0 mr = 2 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.230000 number of dielectric boundary points 67482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 15416 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) : 2.088507 object centre at (A) : 41.53650 15.04450 45.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3537215 0.2647503 midg,1,midg; midg,igrid,midg 0.1993139 9.2127629E-02 1,midg,midg; igrid,midg,midg 0.3221473 0.2364694 gauss-seidel spectral radius is 0.9992859 estimated iterations to convergence 295 setup time was (sec) 2.630000 now iterating at: 05:24:24 rms-change max change #iterations 9.975868 382.2949 at 10iterations 5.906231 138.0497 at 20iterations 3.483246 84.68532 at 30iterations 2.049276 40.89775 at 40iterations 1.203421 26.01598 at 50iterations 0.7059934 13.51490 at 60iterations 0.4115999 8.643336 at 70iterations 0.2416993 4.398129 at 80iterations 0.1411891 2.921152 at 90iterations 8.2518727E-02 1.538740 at 100iterations 4.8407022E-02 0.9787760 at 110iterations 2.8406614E-02 0.4949571 at 120iterations 1.6823828E-02 0.3581352 at 130iterations 1.0149160E-02 0.1730123 at 140iterations 6.2576090E-03 0.1139069 at 150iterations 3.9918250E-03 7.0518494E-02 at 160iterations 2.6989726E-03 5.3791046E-02 at 170iterations 1.9332978E-03 3.6888123E-02 at 180iterations finished qdiffx linear iterations at : 05:24:38 total time elapsed so far: 16.01000 # loops : 180 mean,max change (kT/e) : 1.9332978E-03 3.6888123E-02 energy calculations done at 16.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.26000 DelPhi exited at 05:24:39 16.259u 0.261s 0:17.08 96.6% 0+0k 0+0io 0pf+0w