Sat Oct 8 15:58:19 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 Sat Oct 8 2011 at 15:58:19 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.6413605 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): -17.85600 33.81100 ymin,ymax (A): 2.634000 47.90600 zmin,zma (A): -18.07500 37.43200 x,y,z range (A): 51.66700 45.27200 55.50700 scale (grids/A): 0.6413605 object centre (A): 7.977500 25.27000 9.678502 number of atom coordinates read : 2305 total number of charged atoms : 2241 net assigned charge : 4.906005 assigned positive charge : 345.6640 centred at (gu) : 88.66269 91.46706 89.98214 assigned negative charge : -340.7588 centred at (gu) : 88.60867 91.32965 90.00848 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6408 nv = 96 ne = 84 npr = 45848 no. pairs analyzed = 45848 no. exposed pairs = 2973 no. arc points = 20316 no. surface atoms = 1012 nbur = 1293 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3439 m= 0 mr = 61 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2800000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2088 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0072948E-08 4.4408863E-09 midg,1,midg; midg,igrid,midg -5.3787295E-09 2.9622285E-08 1,midg,midg; igrid,midg,midg 1.8539063E-09 9.7802300E-09 gauss-seidel spectral radius is 0.9873803 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 15:58:20 rms-change max change #iterations 0.1370952 20.92250 at 10iterations 1.3845212E-02 2.042578 at 20iterations 1.5145646E-03 0.2232399 at 30iterations 2.5363272E-04 4.5494080E-02 at 40iterations 6.9163485E-05 1.2702942E-02 at 50iterations finished qdiffx linear iterations at : 15:58:23 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 6.9163485E-05 1.2702942E-02 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 15:58:24 4.546u 0.428s 0:05.31 93.4% 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 Sat Oct 8 2011 at 15:58:24 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.924082 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): -17.85600 33.81100 ymin,ymax (A): 2.634000 47.90600 zmin,zma (A): -18.07500 37.43200 x,y,z range (A): 51.66700 45.27200 55.50700 scale (grids/A): 1.924082 object centre (A): 7.977500 25.27000 9.678502 number of atom coordinates read : 2305 total number of charged atoms : 2241 net assigned charge : 4.906005 assigned positive charge : 345.6640 centred at (gu) : 85.98734 94.40078 89.94599 assigned negative charge : -340.7588 centred at (gu) : 85.82606 93.98880 90.02539 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20316 grid for indexing accessible points = 1.400000 m= 24521 mr = 47839 m= 4098 mr = 17813 m= 284 mr = 2636 m= 7 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 913 time to turn everything in is 0.5800000 number of dielectric boundary points 29909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17654 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) : 0.6413605 object centre at (A) : 7.977500 25.27000 9.678502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7137121E-02 1.4388961E-02 midg,1,midg; midg,igrid,midg -6.3865930E-03 2.9241281E-02 1,midg,midg; igrid,midg,midg -4.7165465E-02 2.4783162E-02 gauss-seidel spectral radius is 0.9986331 estimated iterations to convergence 214 setup time was (sec) 0.9400000 now iterating at: 15:58:25 rms-change max change #iterations 4.066583 196.6029 at 10iterations 1.893879 69.04012 at 20iterations 0.8889458 31.73610 at 30iterations 0.4163352 13.90982 at 40iterations 0.1955611 6.181999 at 50iterations 9.1615431E-02 3.118499 at 60iterations 4.2913061E-02 1.445131 at 70iterations 2.0116610E-02 0.6355886 at 80iterations 9.4755404E-03 0.2975845 at 90iterations 4.4724075E-03 0.1433735 at 100iterations 2.1160857E-03 6.7823410E-02 at 110iterations 1.0172774E-03 3.4524441E-02 at 120iterations finished qdiffx linear iterations at : 15:58:38 total time elapsed so far: 13.51000 # loops : 120 mean,max change (kT/e) : 1.0172774E-03 3.4524441E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 15:58:39 13.705u 0.538s 0:14.54 97.8% 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 Sat Oct 8 2011 at 15:58:39 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.886122 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): -17.85600 33.81100 ymin,ymax (A): 2.634000 47.90600 zmin,zma (A): -18.07500 37.43200 x,y,z range (A): 51.66700 45.27200 55.50700 scale (grids/A): 2.886122 object centre (A): 7.977500 25.27000 9.678502 number of atom coordinates read : 2305 total number of charged atoms : 2241 net assigned charge : 4.906005 assigned positive charge : 345.6640 centred at (gu) : 83.98090 96.60097 89.91897 assigned negative charge : -340.7588 centred at (gu) : 83.73903 95.98318 90.03799 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 160650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20316 grid for indexing accessible points = 1.400000 m= 79540 mr = 116335 m= 28718 mr = 64372 m= 7432 mr = 22955 m= 1137 mr = 5694 m= 78 mr = 786 m= 4 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 2791 time to turn everything in is 1.570000 number of dielectric boundary points 67384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 17927 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) : 1.924082 object centre at (A) : 7.977500 25.27000 9.678502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1871148 0.1483767 midg,1,midg; midg,igrid,midg -9.2765808E-02 0.2367538 1,midg,midg; igrid,midg,midg -0.7989305 0.4419939 gauss-seidel spectral radius is 0.9992571 estimated iterations to convergence 290 setup time was (sec) 2.140000 now iterating at: 15:58:41 rms-change max change #iterations 9.562622 361.7322 at 10iterations 5.616545 147.7549 at 20iterations 3.277536 67.20506 at 30iterations 1.913385 41.71861 at 40iterations 1.110225 24.57458 at 50iterations 0.6445432 15.00713 at 60iterations 0.3727471 7.381577 at 70iterations 0.2151453 4.061415 at 80iterations 0.1243923 2.328583 at 90iterations 7.1599364E-02 1.627419 at 100iterations 4.1264080E-02 0.7425270 at 110iterations 2.3852540E-02 0.4209241 at 120iterations 1.3718891E-02 0.2670479 at 130iterations 7.8896424E-03 0.1480935 at 140iterations 4.5388071E-03 8.2822800E-02 at 150iterations 2.6217645E-03 4.9419403E-02 at 160iterations 1.5161007E-03 2.8862953E-02 at 170iterations 8.8537007E-04 1.8287182E-02 at 180iterations finished qdiffx linear iterations at : 15:59:10 total time elapsed so far: 30.57000 # loops : 180 mean,max change (kT/e) : 8.8537007E-04 1.8287182E-02 energy calculations done at 30.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.77000 DelPhi exited at 15:59:10 30.778u 0.809s 0:31.89 98.9% 0+0k 0+0io 0pf+0w