Sat Oct 8 22:34:51 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 22:34:51 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 = 2338 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: 0.6657317 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): -27.14200 26.33300 ymin,ymax (A): 8.037000 49.70800 zmin,zma (A): -12.95900 39.46400 x,y,z range (A): 53.47500 41.67100 52.42300 scale (grids/A): 0.6657317 object centre (A): -0.4045000 28.87250 13.25250 number of atom coordinates read : 2338 total number of charged atoms : 2203 net assigned charge : 11.50002 assigned positive charge : 341.4683 centred at (gu) : 90.42433 90.99290 92.03999 assigned negative charge : -329.9691 centred at (gu) : 90.45974 90.95259 92.02170 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7242 nv = 96 ne = 84 npr = 46336 no. pairs analyzed = 46336 no. exposed pairs = 3161 no. arc points = 22525 no. surface atoms = 1055 nbur = 1283 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 3810 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.2800000 number of dielectric boundary points 3832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2220 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8361 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0300236E-08 5.6383428E-08 midg,1,midg; midg,igrid,midg 2.1390949E-08 5.0781459E-08 1,midg,midg; igrid,midg,midg 3.7291318E-08 2.9230753E-08 gauss-seidel spectral radius is 0.9882911 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 22:34:52 rms-change max change #iterations 0.1548231 25.94533 at 10iterations 1.6861083E-02 2.461005 at 20iterations 2.0205237E-03 0.2404547 at 30iterations 4.3636168E-04 6.7977905E-02 at 40iterations 1.6312259E-04 2.5046349E-02 at 50iterations finished qdiffx linear iterations at : 22:34:55 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.6312259E-04 2.5046349E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 22:34:56 4.132u 0.250s 0:04.67 93.7% 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 22:34:56 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 = 2338 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: 1.997195 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): -27.14200 26.33300 ymin,ymax (A): 8.037000 49.70800 zmin,zma (A): -12.95900 39.46400 x,y,z range (A): 53.47500 41.67100 52.42300 scale (grids/A): 1.997195 object centre (A): -0.4045000 28.87250 13.25250 number of atom coordinates read : 2338 total number of charged atoms : 2203 net assigned charge : 11.50002 assigned positive charge : 341.4683 centred at (gu) : 91.27271 92.97833 96.11967 assigned negative charge : -329.9691 centred at (gu) : 91.37936 92.85789 96.06502 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76268 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22525 grid for indexing accessible points = 1.400000 m= 28512 mr = 51125 m= 5271 mr = 20683 m= 460 mr = 3318 m= 5 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1769 time to turn everything in is 0.5800000 number of dielectric boundary points 35194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17414 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) : 0.6657317 object centre at (A) : -0.4045000 28.87250 13.25250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4219337E-02 4.0938284E-02 midg,1,midg; midg,igrid,midg 4.6059950E-03 3.2221213E-02 1,midg,midg; igrid,midg,midg 6.3657917E-02 6.3682102E-02 gauss-seidel spectral radius is 0.9987385 estimated iterations to convergence 223 setup time was (sec) 0.9300000 now iterating at: 22:34:57 rms-change max change #iterations 4.290483 233.0555 at 10iterations 2.073635 77.29595 at 20iterations 0.9957349 36.74619 at 30iterations 0.4792489 14.18657 at 40iterations 0.2312332 7.450402 at 50iterations 0.1115607 3.346337 at 60iterations 5.3836267E-02 1.729885 at 70iterations 2.6032111E-02 0.8296716 at 80iterations 1.2565294E-02 0.4133921 at 90iterations 6.0973302E-03 0.2051773 at 100iterations 3.0251746E-03 9.0150356E-02 at 110iterations 1.5371429E-03 4.7295570E-02 at 120iterations finished qdiffx linear iterations at : 22:35:05 total time elapsed so far: 9.480000 # loops : 120 mean,max change (kT/e) : 1.5371429E-03 4.7295570E-02 energy calculations done at 9.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 22:35:06 9.660u 0.249s 0:10.23 96.7% 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 22:35:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2338 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: 2.995793 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): -27.14200 26.33300 ymin,ymax (A): 8.037000 49.70800 zmin,zma (A): -12.95900 39.46400 x,y,z range (A): 53.47500 41.67100 52.42300 scale (grids/A): 2.995793 object centre (A): -0.4045000 28.87250 13.25250 number of atom coordinates read : 2338 total number of charged atoms : 2203 net assigned charge : 11.50002 assigned positive charge : 341.4683 centred at (gu) : 91.90905 94.46735 99.17936 assigned negative charge : -329.9691 centred at (gu) : 92.06902 94.28679 99.09753 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 176240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22525 grid for indexing accessible points = 1.400000 m= 89626 mr = 124389 m= 35056 mr = 72310 m= 9773 mr = 27895 m= 1816 mr = 7360 m= 178 mr = 1280 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 5918 time to turn everything in is 1.540000 number of dielectric boundary points 79362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 17624 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) : 1.997195 object centre at (A) : -0.4045000 28.87250 13.25250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5447338 0.3999985 midg,1,midg; midg,igrid,midg 1.5664924E-02 0.3113357 1,midg,midg; igrid,midg,midg 0.6427954 0.5705608 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.880000 now iterating at: 22:35:08 rms-change max change #iterations 10.06559 438.6065 at 10iterations 6.019240 135.4332 at 20iterations 3.594240 72.05568 at 30iterations 2.134824 41.83373 at 40iterations 1.261634 25.23219 at 50iterations 0.7449015 15.64653 at 60iterations 0.4379587 9.766491 at 70iterations 0.2571665 4.760546 at 80iterations 0.1508377 2.748191 at 90iterations 8.8398084E-02 1.715035 at 100iterations 5.1809091E-02 0.9389076 at 110iterations 3.0268874E-02 0.6553411 at 120iterations 1.7781429E-02 0.3047273 at 130iterations 1.0395258E-02 0.1909871 at 140iterations 6.1309687E-03 0.1062479 at 150iterations 3.6588188E-03 7.3390961E-02 at 160iterations 2.2182318E-03 5.3358078E-02 at 170iterations 1.3948896E-03 2.7923584E-02 at 180iterations finished qdiffx linear iterations at : 22:35:22 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 1.3948896E-03 2.7923584E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.64000 DelPhi exited at 22:35:22 15.644u 0.258s 0:16.22 97.9% 0+0k 0+0io 0pf+0w