Sat Oct 8 21:39:34 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 Sat Oct 8 2011 at 21:39:34 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 = 2025 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: 0.6620176 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): 5.937000 59.71200 ymin,ymax (A): 2.951000 50.19800 zmin,zma (A): 14.67600 56.02900 x,y,z range (A): 53.77500 47.24700 41.35300 scale (grids/A): 0.6620176 object centre (A): 32.82450 26.57450 35.35250 number of atom coordinates read : 2025 total number of charged atoms : 1889 net assigned charge : 3.0249357E-06 assigned positive charge : 300.5608 centred at (gu) : 87.81039 89.32217 88.98096 assigned negative charge : -300.5609 centred at (gu) : 87.92672 89.35764 89.01617 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6030 nv = 96 ne = 84 npr = 40360 no. pairs analyzed = 40360 no. exposed pairs = 2652 no. arc points = 18530 no. surface atoms = 887 nbur = 1138 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3253 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1664 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6919 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3017307E-09 -5.0180673E-09 midg,1,midg; midg,igrid,midg 5.9066187E-09 -5.4275775E-09 1,midg,midg; igrid,midg,midg 2.8594110E-08 -1.2297061E-08 gauss-seidel spectral radius is 0.9881232 estimated iterations to convergence 75 setup time was (sec) 0.3500000 now iterating at: 21:39:34 rms-change max change #iterations 0.1464120 24.61496 at 10iterations 1.5458773E-02 2.798958 at 20iterations 1.6703053E-03 0.2290258 at 30iterations 1.7944450E-04 3.3016205E-02 at 40iterations 2.1655087E-05 3.3416748E-03 at 50iterations finished qdiffx linear iterations at : 21:39:37 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.1655087E-05 3.3416748E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 21:39:38 3.338u 0.169s 0:03.79 92.0% 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 Sat Oct 8 2011 at 21:39:38 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 = 2025 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: 1.986053 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): 5.937000 59.71200 ymin,ymax (A): 2.951000 50.19800 zmin,zma (A): 14.67600 56.02900 x,y,z range (A): 53.77500 47.24700 41.35300 scale (grids/A): 1.986053 object centre (A): 32.82450 26.57450 35.35250 number of atom coordinates read : 2025 total number of charged atoms : 1889 net assigned charge : 3.0249357E-06 assigned positive charge : 300.5608 centred at (gu) : 83.43086 87.96651 86.94292 assigned negative charge : -300.5609 centred at (gu) : 83.78007 88.07282 87.04865 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18530 grid for indexing accessible points = 1.400000 m= 23673 mr = 44178 m= 4127 mr = 17196 m= 294 mr = 2583 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 251 time to turn everything in is 0.3300000 number of dielectric boundary points 28625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14941 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) : 0.6620176 object centre at (A) : 32.82450 26.57450 35.35250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5394736E-03 -1.6802270E-03 midg,1,midg; midg,igrid,midg 2.3107765E-02 1.7931110E-03 1,midg,midg; igrid,midg,midg -4.1526768E-02 -4.4096280E-02 gauss-seidel spectral radius is 0.9986840 estimated iterations to convergence 218 setup time was (sec) 0.5400000 now iterating at: 21:39:38 rms-change max change #iterations 4.016870 222.7805 at 10iterations 1.909722 69.16003 at 20iterations 0.9042948 32.34913 at 30iterations 0.4301798 14.59624 at 40iterations 0.2045677 7.250231 at 50iterations 9.7001210E-02 3.144682 at 60iterations 4.5901369E-02 1.497547 at 70iterations 2.1875633E-02 0.7125993 at 80iterations 1.0398927E-02 0.3387241 at 90iterations 4.9463748E-03 0.1595383 at 100iterations 2.3537949E-03 7.9881668E-02 at 110iterations 1.1157179E-03 4.1145325E-02 at 120iterations finished qdiffx linear iterations at : 21:39:45 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 1.1157179E-03 4.1145325E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 21:39:46 7.653u 0.207s 0:08.27 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 Sat Oct 8 2011 at 21:39:46 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 = 2025 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: 2.979079 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): 5.937000 59.71200 ymin,ymax (A): 2.951000 50.19800 zmin,zma (A): 14.67600 56.02900 x,y,z range (A): 53.77500 47.24700 41.35300 scale (grids/A): 2.979079 object centre (A): 32.82450 26.57450 35.35250 number of atom coordinates read : 2025 total number of charged atoms : 1889 net assigned charge : 3.0249357E-06 assigned positive charge : 300.5608 centred at (gu) : 80.14632 86.94970 85.41421 assigned negative charge : -300.5609 centred at (gu) : 80.67014 87.10924 85.57294 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 149262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18530 grid for indexing accessible points = 1.400000 m= 75199 mr = 107097 m= 28482 mr = 60875 m= 7608 mr = 22714 m= 1332 mr = 5732 m= 86 mr = 914 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 744 time to turn everything in is 0.8500000 number of dielectric boundary points 64606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 15112 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) : 1.986053 object centre at (A) : 32.82450 26.57450 35.35250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9050072E-02 -1.8105252E-02 midg,1,midg; midg,igrid,midg 0.2292685 -5.7395212E-02 1,midg,midg; igrid,midg,midg -0.6569565 -0.5818194 gauss-seidel spectral radius is 0.9992635 estimated iterations to convergence 291 setup time was (sec) 1.070000 now iterating at: 21:39:47 rms-change max change #iterations 9.381396 411.7013 at 10iterations 5.529312 136.5595 at 20iterations 3.234357 86.28712 at 30iterations 1.888175 38.99749 at 40iterations 1.099323 21.67833 at 50iterations 0.6385567 12.95194 at 60iterations 0.3697148 7.492146 at 70iterations 0.2145438 4.489576 at 80iterations 0.1235392 2.391493 at 90iterations 7.1561120E-02 1.315964 at 100iterations 4.1212164E-02 0.7395153 at 110iterations 2.3796998E-02 0.4502964 at 120iterations 1.3712676E-02 0.2639503 at 130iterations 7.9387175E-03 0.1522846 at 140iterations 4.5717545E-03 9.5167041E-02 at 150iterations 2.6562263E-03 5.2392960E-02 at 160iterations 1.5419797E-03 2.8259277E-02 at 170iterations 8.9752488E-04 1.7842293E-02 at 180iterations finished qdiffx linear iterations at : 21:39:58 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 8.9752488E-04 1.7842293E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 21:39:59 12.213u 0.210s 0:12.71 97.7% 0+0k 0+0io 0pf+0w