Tue Nov 22 14:10:17 PST 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 Nov 22 2011 at 14:10:25 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 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: 0.6465791 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): -5.544000 34.69600 ymin,ymax (A): -3.383000 49.42200 zmin,zma (A): -8.212000 46.84700 x,y,z range (A): 40.24000 52.80500 55.05900 scale (grids/A): 0.6465791 object centre (A): 14.57600 23.01950 19.31750 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 286.9601 centred at (gu) : 89.44357 92.10677 90.09561 assigned negative charge : -281.9603 centred at (gu) : 89.37093 92.20972 90.14410 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5554 nv = 96 ne = 84 npr = 40473 no. pairs analyzed = 40473 no. exposed pairs = 2507 no. arc points = 17629 no. surface atoms = 849 nbur = 1107 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 269 mr = 3012 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1600000 number of dielectric boundary points 2779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1823 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6577 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3619030E-08 4.2105519E-09 midg,1,midg; midg,igrid,midg 1.2437166E-08 -2.6337474E-09 1,midg,midg; igrid,midg,midg 1.8206404E-09 1.4502075E-08 gauss-seidel spectral radius is 0.9875497 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 14:10:28 rms-change max change #iterations 0.1303194 21.16095 at 10iterations 1.3013167E-02 2.404739 at 20iterations 1.3065233E-03 0.2431302 at 30iterations 1.3207375E-04 2.3368835E-02 at 40iterations 1.3019368E-05 1.8701553E-03 at 50iterations finished qdiffx linear iterations at : 14:10:38 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.3019368E-05 1.8701553E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 14:10:39 3.576u 0.225s 0:15.00 25.2% 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 Tue Nov 22 2011 at 14:10:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 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: 1.939737 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): -5.544000 34.69600 ymin,ymax (A): -3.383000 49.42200 zmin,zma (A): -8.212000 46.84700 x,y,z range (A): 40.24000 52.80500 55.05900 scale (grids/A): 1.939737 object centre (A): 14.57600 23.01950 19.31750 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 286.9601 centred at (gu) : 88.33084 96.32029 90.28707 assigned negative charge : -281.9603 centred at (gu) : 88.11297 96.62942 90.43246 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 59841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17629 grid for indexing accessible points = 1.400000 m= 21172 mr = 40829 m= 3001 mr = 15891 m= 120 mr = 1898 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 214 time to turn everything in is 0.3100000 number of dielectric boundary points 25484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14391 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) : 0.6465791 object centre at (A) : 14.57600 23.01950 19.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2573675E-02 4.5493875E-02 midg,1,midg; midg,igrid,midg 3.4408484E-02 4.6155769E-03 1,midg,midg; igrid,midg,midg 8.0378661E-03 7.7315350E-03 gauss-seidel spectral radius is 0.9986075 estimated iterations to convergence 212 setup time was (sec) 0.5500000 now iterating at: 14:10:46 rms-change max change #iterations 3.659464 182.5284 at 10iterations 1.705545 78.33176 at 20iterations 0.7929053 30.74444 at 30iterations 0.3682610 13.42249 at 40iterations 0.1706616 5.888747 at 50iterations 7.9285994E-02 2.879349 at 60iterations 3.6768056E-02 1.279076 at 70iterations 1.7046096E-02 0.6265450 at 80iterations 7.9265768E-03 0.2870255 at 90iterations 3.6726212E-03 0.1283875 at 100iterations 1.7058396E-03 5.7983398E-02 at 110iterations 7.9588417E-04 2.6925802E-02 at 120iterations finished qdiffx linear iterations at : 14:11:06 total time elapsed so far: 8.580000 # loops : 120 mean,max change (kT/e) : 7.9588417E-04 2.6925802E-02 energy calculations done at 8.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 14:11:08 8.711u 0.237s 0:27.45 32.5% 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 Nov 22 2011 at 14:11:10 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 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: 2.909606 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): -5.544000 34.69600 ymin,ymax (A): -3.383000 49.42200 zmin,zma (A): -8.212000 46.84700 x,y,z range (A): 40.24000 52.80500 55.05900 scale (grids/A): 2.909606 object centre (A): 14.57600 23.01950 19.31750 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 286.9601 centred at (gu) : 87.49622 99.48052 90.43051 assigned negative charge : -281.9603 centred at (gu) : 87.16943 99.94422 90.64880 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 138354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17629 grid for indexing accessible points = 1.400000 m= 68960 mr = 98791 m= 24308 mr = 56867 m= 5397 mr = 19925 m= 674 mr = 4139 m= 16 mr = 482 m= 0 mr = 1 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 720 time to turn everything in is 0.8200000 number of dielectric boundary points 57504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14592 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) : 1.939737 object centre at (A) : 14.57600 23.01950 19.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6815456E-03 0.8412277 midg,1,midg; midg,igrid,midg 0.3548019 -8.9700874E-03 1,midg,midg; igrid,midg,midg 0.1496080 4.7782701E-02 gauss-seidel spectral radius is 0.9992406 estimated iterations to convergence 286 setup time was (sec) 1.100000 now iterating at: 14:11:17 rms-change max change #iterations 8.559932 408.2665 at 10iterations 4.935737 134.2553 at 20iterations 2.823780 60.56010 at 30iterations 1.614590 36.09598 at 40iterations 0.9227679 19.40574 at 50iterations 0.5268838 11.33504 at 60iterations 0.2994538 6.020230 at 70iterations 0.1707913 3.434635 at 80iterations 9.7464666E-02 1.869659 at 90iterations 5.5417523E-02 1.163208 at 100iterations 3.1512808E-02 0.6027737 at 110iterations 1.7960696E-02 0.3742294 at 120iterations 1.0222291E-02 0.2111715 at 130iterations 5.8137947E-03 0.1182899 at 140iterations 3.3101260E-03 6.7527771E-02 at 150iterations 1.8843005E-03 3.8277984E-02 at 160iterations 1.0724467E-03 2.0133972E-02 at 170iterations 6.1098463E-04 1.3108253E-02 at 180iterations finished qdiffx linear iterations at : 14:11:57 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 6.1098463E-04 1.3108253E-02 energy calculations done at 14.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.50000 DelPhi exited at 14:12:00 14.501u 0.294s 0:50.40 29.3% 0+0k 0+0io 0pf+0w