Mon Oct 10 19:39:21 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 19:39:21 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 = 2379 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: 0.6105718 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): 17.52700 70.27200 ymin,ymax (A): -36.67700 8.163000 zmin,zma (A): -25.91400 32.39200 x,y,z range (A): 52.74500 44.84000 58.30600 scale (grids/A): 0.6105718 object centre (A): 43.89950 -14.25700 3.239001 number of atom coordinates read : 2379 total number of charged atoms : 2245 net assigned charge : 6.500019 assigned positive charge : 353.5833 centred at (gu) : 90.54546 89.49561 89.08373 assigned negative charge : -347.0837 centred at (gu) : 90.48741 89.61828 89.23615 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5977 nv = 96 ne = 84 npr = 47200 no. pairs analyzed = 47200 no. exposed pairs = 3256 no. arc points = 23087 no. surface atoms = 1092 nbur = 1287 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 277 mr = 2957 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.3000000 number of dielectric boundary points 3279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2317 ## 238 charges are in solution ## iepsmp to db, and charging done at 2.540000 number of grid points assigned charge 7304 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2942866E-08 -2.5536766E-09 midg,1,midg; midg,igrid,midg 1.0340639E-08 -1.5880399E-09 1,midg,midg; igrid,midg,midg 1.0508731E-09 7.2095858E-09 gauss-seidel spectral radius is 0.9861022 estimated iterations to convergence 69 setup time was (sec) 2.750000 now iterating at: 19:39:24 rms-change max change #iterations 0.1084979 19.45269 at 10iterations 9.6355323E-03 1.606743 at 20iterations 8.8787777E-04 0.1519742 at 30iterations 8.5694039E-05 1.3984680E-02 at 40iterations 1.0402528E-05 1.8615723E-03 at 50iterations finished qdiffx linear iterations at : 19:39:28 total time elapsed so far: 6.880000 # loops : 50 mean,max change (kT/e) : 1.0402528E-05 1.8615723E-03 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 19:39:29 7.057u 0.362s 0:07.70 96.2% 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 19:39:29 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 = 2379 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.831715 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): 17.52700 70.27200 ymin,ymax (A): -36.67700 8.163000 zmin,zma (A): -25.91400 32.39200 x,y,z range (A): 52.74500 44.84000 58.30600 scale (grids/A): 1.831715 object centre (A): 43.89950 -14.25700 3.239001 number of atom coordinates read : 2379 total number of charged atoms : 2245 net assigned charge : 6.500019 assigned positive charge : 353.5833 centred at (gu) : 91.63600 88.48650 87.25052 assigned negative charge : -347.0837 centred at (gu) : 91.46194 88.85461 87.70834 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 64230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23087 grid for indexing accessible points = 1.400000 m= 21075 mr = 42003 m= 2940 mr = 14508 m= 149 mr = 1592 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 302 time to turn everything in is 0.5600000 number of dielectric boundary points 30250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17608 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) : 0.6105718 object centre at (A) : 43.89950 -14.25700 3.239001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7639733E-02 -2.5082488E-02 midg,1,midg; midg,igrid,midg 1.9493207E-02 -2.0592595E-03 1,midg,midg; igrid,midg,midg 2.1492340E-02 2.1722693E-02 gauss-seidel spectral radius is 0.9985151 estimated iterations to convergence 206 setup time was (sec) 0.8400000 now iterating at: 19:39:30 rms-change max change #iterations 3.659770 164.0520 at 10iterations 1.659168 58.49662 at 20iterations 0.7491633 29.70656 at 30iterations 0.3383368 12.73873 at 40iterations 0.1523860 4.960135 at 50iterations 6.9297090E-02 2.416412 at 60iterations 3.1362779E-02 1.102632 at 70iterations 1.4165433E-02 0.4855404 at 80iterations 6.4174114E-03 0.2508621 at 90iterations 2.9066883E-03 9.9729538E-02 at 100iterations 1.3162976E-03 4.9160004E-02 at 110iterations 5.9827371E-04 2.0813942E-02 at 120iterations finished qdiffx linear iterations at : 19:39:41 total time elapsed so far: 11.45000 # loops : 120 mean,max change (kT/e) : 5.9827371E-04 2.0813942E-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 19:39:41 11.619u 0.478s 0:12.39 97.4% 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 Mon Oct 10 2011 at 19:39:41 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 = 2379 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: 2.747573 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): 17.52700 70.27200 ymin,ymax (A): -36.67700 8.163000 zmin,zma (A): -25.91400 32.39200 x,y,z range (A): 52.74500 44.84000 58.30600 scale (grids/A): 2.747573 object centre (A): 43.89950 -14.25700 3.239001 number of atom coordinates read : 2379 total number of charged atoms : 2245 net assigned charge : 6.500019 assigned positive charge : 353.5833 centred at (gu) : 92.45398 87.72965 85.87578 assigned negative charge : -347.0837 centred at (gu) : 92.19289 88.28199 86.56242 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 148667 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23087 grid for indexing accessible points = 1.400000 m= 69657 mr = 102675 m= 23234 mr = 54712 m= 4787 mr = 17764 m= 578 mr = 3286 m= 20 mr = 337 m= 0 mr = 4 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 949 time to turn everything in is 1.340000 number of dielectric boundary points 68165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 17959 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) : 1.831715 object centre at (A) : 43.89950 -14.25700 3.239001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7048194 -5.5780172E-02 midg,1,midg; midg,igrid,midg 0.2445644 -5.4404465E-03 1,midg,midg; igrid,midg,midg 0.1818597 0.1761288 gauss-seidel spectral radius is 0.9992356 estimated iterations to convergence 285 setup time was (sec) 1.660000 now iterating at: 19:39:43 rms-change max change #iterations 8.963060 267.6421 at 10iterations 5.229708 126.5814 at 20iterations 3.032774 72.44996 at 30iterations 1.743054 36.50034 at 40iterations 1.002494 22.57944 at 50iterations 0.5753374 11.86945 at 60iterations 0.3288817 7.094681 at 70iterations 0.1882997 3.881409 at 80iterations 0.1074363 2.523563 at 90iterations 6.1202615E-02 1.427658 at 100iterations 3.4925409E-02 0.6913185 at 110iterations 1.9909203E-02 0.4001312 at 120iterations 1.1323282E-02 0.2273774 at 130iterations 6.4427783E-03 0.1424026 at 140iterations 3.6726643E-03 7.4013710E-02 at 150iterations 2.0916355E-03 4.2251587E-02 at 160iterations 1.1901429E-03 2.1575928E-02 at 170iterations 6.7648664E-04 1.2304306E-02 at 180iterations finished qdiffx linear iterations at : 19:40:00 total time elapsed so far: 18.54000 # loops : 180 mean,max change (kT/e) : 6.7648664E-04 1.2304306E-02 energy calculations done at 18.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.70000 DelPhi exited at 19:40:02 18.707u 0.472s 0:20.85 91.9% 0+0k 0+0io 0pf+0w