Tue Oct 11 06:09:48 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 Tue Oct 11 2011 at 06:09:48 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 = 2070 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: 0.6862916 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): 19.52400 63.73700 ymin,ymax (A): 32.15400 84.02700 zmin,zma (A): 58.35600 97.96000 x,y,z range (A): 44.21300 51.87300 39.60400 scale (grids/A): 0.6862916 object centre (A): 41.63050 58.09050 78.15800 number of atom coordinates read : 2070 total number of charged atoms : 1942 net assigned charge : 7.500009 assigned positive charge : 313.8370 centred at (gu) : 89.68993 90.14962 88.90019 assigned negative charge : -306.3372 centred at (gu) : 89.82578 90.18440 88.83141 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6562 nv = 96 ne = 84 npr = 42117 no. pairs analyzed = 42117 no. exposed pairs = 2486 no. arc points = 16997 no. surface atoms = 863 nbur = 1207 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 384 mr = 3735 m= 5 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1678 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7505 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1070448E-08 4.6995947E-08 midg,1,midg; midg,igrid,midg 4.6886289E-08 2.8323395E-08 1,midg,midg; igrid,midg,midg 8.2876291E-08 -2.8147717E-09 gauss-seidel spectral radius is 0.9889362 estimated iterations to convergence 77 setup time was (sec) 0.4800000 now iterating at: 06:09:49 rms-change max change #iterations 0.1732336 23.42774 at 10iterations 2.0435132E-02 2.504710 at 20iterations 2.5836036E-03 0.4051394 at 30iterations 4.3237742E-04 6.6864014E-02 at 40iterations 1.0534331E-04 1.3408661E-02 at 50iterations finished qdiffx linear iterations at : 06:09:51 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.0534331E-04 1.3408661E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 06:09:52 3.075u 0.133s 0:03.50 91.4% 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 Tue Oct 11 2011 at 06:09:52 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 = 2070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.058875 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): 19.52400 63.73700 ymin,ymax (A): 32.15400 84.02700 zmin,zma (A): 58.35600 97.96000 x,y,z range (A): 44.21300 51.87300 39.60400 scale (grids/A): 2.058875 object centre (A): 41.63050 58.09050 78.15800 number of atom coordinates read : 2070 total number of charged atoms : 1942 net assigned charge : 7.500009 assigned positive charge : 313.8370 centred at (gu) : 89.06966 90.44895 86.70082 assigned negative charge : -306.3372 centred at (gu) : 89.47749 90.55350 86.49434 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16997 grid for indexing accessible points = 1.400000 m= 27499 mr = 49506 m= 4814 mr = 20614 m= 369 mr = 2955 m= 10 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 559 time to turn everything in is 0.5400000 number of dielectric boundary points 29129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15382 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) : 0.6862916 object centre at (A) : 41.63050 58.09050 78.15800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7230378E-02 1.2143360E-02 midg,1,midg; midg,igrid,midg 2.3182875E-02 2.4737550E-02 1,midg,midg; igrid,midg,midg 5.8120202E-02 7.1511166E-03 gauss-seidel spectral radius is 0.9987642 estimated iterations to convergence 225 setup time was (sec) 0.8200000 now iterating at: 06:09:53 rms-change max change #iterations 4.328682 181.5798 at 10iterations 2.117443 68.32350 at 20iterations 1.029741 32.75298 at 30iterations 0.5025594 15.58197 at 40iterations 0.2456328 7.962499 at 50iterations 0.1200011 4.173792 at 60iterations 5.8580115E-02 1.753231 at 70iterations 2.8622972E-02 0.8699976 at 80iterations 1.3994578E-02 0.4631348 at 90iterations 6.8663652E-03 0.2184725 at 100iterations 3.4104479E-03 0.1207809 at 110iterations 1.7116475E-03 5.5153608E-02 at 120iterations finished qdiffx linear iterations at : 06:09:59 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 1.7116475E-03 5.5153608E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 06:09:59 7.129u 0.194s 0:07.71 94.8% 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 Tue Oct 11 2011 at 06:09:59 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 = 2070 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.088312 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): 19.52400 63.73700 ymin,ymax (A): 32.15400 84.02700 zmin,zma (A): 58.35600 97.96000 x,y,z range (A): 44.21300 51.87300 39.60400 scale (grids/A): 3.088312 object centre (A): 41.63050 58.09050 78.15800 number of atom coordinates read : 2070 total number of charged atoms : 1942 net assigned charge : 7.500009 assigned positive charge : 313.8370 centred at (gu) : 88.60449 90.67334 85.05109 assigned negative charge : -306.3372 centred at (gu) : 89.21618 90.83040 84.74157 start vw surface at 0.1400000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 160605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16997 grid for indexing accessible points = 1.400000 m= 86620 mr = 119201 m= 33897 mr = 71941 m= 8829 mr = 27365 m= 1440 mr = 6394 m= 171 mr = 954 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 1780 time to turn everything in is 1.620000 number of dielectric boundary points 65625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 15536 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) : 2.058875 object centre at (A) : 41.63050 58.09050 78.15800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2645646 4.8074692E-02 midg,1,midg; midg,igrid,midg 0.1726621 0.1918374 1,midg,midg; igrid,midg,midg 0.6837699 3.6013480E-02 gauss-seidel spectral radius is 0.9992767 estimated iterations to convergence 293 setup time was (sec) 1.930000 now iterating at: 06:10:01 rms-change max change #iterations 9.787460 359.8817 at 10iterations 5.739637 160.0106 at 20iterations 3.363166 65.60786 at 30iterations 1.966270 51.68629 at 40iterations 1.150252 23.98306 at 50iterations 0.6683594 12.59794 at 60iterations 0.3894514 7.496147 at 70iterations 0.2271369 4.087788 at 80iterations 0.1320048 2.809057 at 90iterations 7.6696306E-02 1.562586 at 100iterations 4.4547189E-02 0.7934322 at 110iterations 2.6021140E-02 0.4700561 at 120iterations 1.5208215E-02 0.3157597 at 130iterations 8.9835282E-03 0.1693258 at 140iterations 5.3765466E-03 0.1059189 at 150iterations 3.3050207E-03 6.2421799E-02 at 160iterations 2.1256867E-03 3.9642334E-02 at 170iterations 1.4392933E-03 2.6992798E-02 at 180iterations finished qdiffx linear iterations at : 06:10:12 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 1.4392933E-03 2.6992798E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 06:10:13 12.717u 0.279s 0:13.69 94.8% 0+0k 0+0io 0pf+0w