Tue Oct 11 06:11:45 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+sph2.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 = amb2.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 06:11:45 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2043 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: 0.7043368 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): 27.06500 70.73000 ymin,ymax (A): 43.91700 82.06900 zmin,zma (A): -60.27600 -9.732000 x,y,z range (A): 43.66500 38.15200 50.54400 scale (grids/A): 0.7043368 object centre (A): 48.89750 62.99300 -35.00400 number of atom coordinates read : 2043 total number of charged atoms : 1913 net assigned charge : 5.500006 assigned positive charge : 309.1621 centred at (gu) : 90.59198 89.49141 89.08813 assigned negative charge : -303.6622 centred at (gu) : 90.74242 89.57317 89.11175 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7024 nv = 96 ne = 84 npr = 40592 no. pairs analyzed = 40592 no. exposed pairs = 2625 no. arc points = 17565 no. surface atoms = 883 nbur = 1160 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 509 mr = 4014 m= 6 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 9.0000018E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1590 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4132159E-08 2.7608756E-08 midg,1,midg; midg,igrid,midg 8.7918551E-08 5.9231864E-09 1,midg,midg; igrid,midg,midg 9.7753244E-08 -2.8770726E-08 gauss-seidel spectral radius is 0.9894919 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 06:11:45 rms-change max change #iterations 0.1955228 27.12904 at 10iterations 2.4847882E-02 3.246903 at 20iterations 3.6580632E-03 0.5159397 at 30iterations 8.8545622E-04 0.1083717 at 40iterations 3.0422359E-04 3.8585663E-02 at 50iterations finished qdiffx linear iterations at : 06:11:48 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 3.0422359E-04 3.8585663E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 06:11:49 3.634u 0.212s 0:04.39 87.4% 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 06:11:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2043 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: 2.113010 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): 27.06500 70.73000 ymin,ymax (A): 43.91700 82.06900 zmin,zma (A): -60.27600 -9.732000 x,y,z range (A): 43.66500 38.15200 50.54400 scale (grids/A): 2.113010 object centre (A): 48.89750 62.99300 -35.00400 number of atom coordinates read : 2043 total number of charged atoms : 1913 net assigned charge : 5.500006 assigned positive charge : 309.1621 centred at (gu) : 91.77585 88.47408 87.26435 assigned negative charge : -303.6622 centred at (gu) : 92.22739 88.71957 87.33535 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17565 grid for indexing accessible points = 1.400000 m= 30820 mr = 52257 m= 6267 mr = 23359 m= 611 mr = 4204 m= 18 mr = 285 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 31414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15162 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) : 0.7043368 object centre at (A) : 48.89750 62.99300 -35.00400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2227287E-02 1.9475348E-02 midg,1,midg; midg,igrid,midg 3.2908902E-02 -4.2751860E-03 1,midg,midg; igrid,midg,midg 3.6826361E-02 7.6703415E-03 gauss-seidel spectral radius is 0.9988227 estimated iterations to convergence 231 setup time was (sec) 0.8900000 now iterating at: 06:11:50 rms-change max change #iterations 4.514234 181.4946 at 10iterations 2.241610 73.16849 at 20iterations 1.106097 33.87234 at 30iterations 0.5460879 18.00259 at 40iterations 0.2716461 8.732303 at 50iterations 0.1343338 4.025909 at 60iterations 6.6996098E-02 2.175407 at 70iterations 3.3344053E-02 0.9170055 at 80iterations 1.6674396E-02 0.5010872 at 90iterations 8.5349251E-03 0.2641792 at 100iterations 4.4128783E-03 0.1657162 at 110iterations 2.4283743E-03 8.8878632E-02 at 120iterations finished qdiffx linear iterations at : 06:11:58 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 2.4283743E-03 8.8878632E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 06:11:58 8.497u 0.272s 0:09.26 94.6% 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 06:11:59 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2043 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: 3.169516 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): 27.06500 70.73000 ymin,ymax (A): 43.91700 82.06900 zmin,zma (A): -60.27600 -9.732000 x,y,z range (A): 43.66500 38.15200 50.54400 scale (grids/A): 3.169516 object centre (A): 48.89750 62.99300 -35.00400 number of atom coordinates read : 2043 total number of charged atoms : 1913 net assigned charge : 5.500006 assigned positive charge : 309.1621 centred at (gu) : 92.66377 87.71129 85.89661 assigned negative charge : -303.6622 centred at (gu) : 93.34115 88.07931 86.00305 start vw surface at 0.1200000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 169963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17565 grid for indexing accessible points = 1.400000 m= 94682 mr = 125690 m= 39990 mr = 78715 m= 11959 mr = 32881 m= 2325 mr = 9244 m= 252 mr = 1639 m= 4 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 70879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 15304 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) : 2.113010 object centre at (A) : 48.89750 62.99300 -35.00400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2902794 -5.7637874E-02 midg,1,midg; midg,igrid,midg 0.2723751 -3.6325254E-02 1,midg,midg; igrid,midg,midg 0.3106951 0.1667762 gauss-seidel spectral radius is 0.9992938 estimated iterations to convergence 297 setup time was (sec) 2.090000 now iterating at: 06:12:01 rms-change max change #iterations 10.15419 308.3156 at 10iterations 6.046659 124.9793 at 20iterations 3.595555 71.95535 at 30iterations 2.122432 40.66468 at 40iterations 1.253409 24.26900 at 50iterations 0.7373905 13.87224 at 60iterations 0.4337279 8.254532 at 70iterations 0.2544127 4.650996 at 80iterations 0.1496108 2.955244 at 90iterations 8.7749153E-02 1.824780 at 100iterations 5.1677126E-02 0.9060669 at 110iterations 3.0631887E-02 0.5999413 at 120iterations 1.8401435E-02 0.3476563 at 130iterations 1.1290255E-02 0.2048435 at 140iterations 7.2563156E-03 0.1380291 at 150iterations 4.9160714E-03 0.1004105 at 160iterations 3.5655324E-03 6.3976288E-02 at 170iterations 2.7588073E-03 4.6539307E-02 at 180iterations finished qdiffx linear iterations at : 06:12:11 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 2.7588073E-03 4.6539307E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 06:12:12 12.808u 0.288s 0:13.78 94.9% 0+0k 0+0io 0pf+0w