Sat Oct 8 11:45:35 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 Sat Oct 8 2011 at 11:45:35 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4433 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 0.5614079 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): -27.25700 35.12900 ymin,ymax (A): 34.69100 98.10300 zmin,zma (A): 30.99300 90.89100 x,y,z range (A): 62.38600 63.41201 59.89799 scale (grids/A): 0.5614079 object centre (A): 3.935999 66.39700 60.94200 number of atom coordinates read : 4433 total number of charged atoms : 4273 net assigned charge : -7.485951 assigned positive charge : 667.9782 centred at (gu) : 90.80157 88.45071 88.71589 assigned negative charge : -675.4673 centred at (gu) : 90.67879 88.50747 88.87178 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8841 nv = 96 ne = 84 npr = 93636 no. pairs analyzed = 93636 no. exposed pairs = 4949 no. arc points = 33719 no. surface atoms = 1686 nbur = 2747 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 392 mr = 5116 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.3200000 number of dielectric boundary points 4085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3541 ## 443 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11835 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4730007E-09 -2.7197486E-09 midg,1,midg; midg,igrid,midg 1.4880179E-10 -1.3234801E-09 1,midg,midg; igrid,midg,midg -2.5574278E-09 1.5007640E-09 gauss-seidel spectral radius is 0.9837333 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 11:45:36 rms-change max change #iterations 0.1061011 15.22765 at 10iterations 8.2153315E-03 1.098488 at 20iterations 1.0286768E-03 0.1677361 at 30iterations 2.6290343E-04 4.4086456E-02 at 40iterations 8.3773732E-05 1.1882782E-02 at 50iterations finished qdiffx linear iterations at : 11:45:40 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 8.3773732E-05 1.1882782E-02 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 11:45:41 4.488u 0.276s 0:05.76 82.4% 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 Sat Oct 8 2011 at 11:45:41 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4433 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 1.684224 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): -27.25700 35.12900 ymin,ymax (A): 34.69100 98.10300 zmin,zma (A): 30.99300 90.89100 x,y,z range (A): 62.38600 63.41201 59.89799 scale (grids/A): 1.684224 object centre (A): 3.935999 66.39700 60.94200 number of atom coordinates read : 4433 total number of charged atoms : 4273 net assigned charge : -7.485951 assigned positive charge : 667.9782 centred at (gu) : 92.40353 85.35108 86.14626 assigned negative charge : -675.4673 centred at (gu) : 92.03587 85.52198 86.61497 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 99576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33719 grid for indexing accessible points = 1.400000 m= 33216 mr = 72363 m= 4091 mr = 24359 m= 125 mr = 2417 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 7016 time to turn everything in is 0.4900000 number of dielectric boundary points 37851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 404 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 33006 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) : 0.5614079 object centre at (A) : 3.935999 66.39700 60.94200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8654370E-02 -2.4583274E-02 midg,1,midg; midg,igrid,midg 1.3861927E-02 -7.7205873E-03 1,midg,midg; igrid,midg,midg -2.6659612E-02 2.4218258E-02 gauss-seidel spectral radius is 0.9984205 estimated iterations to convergence 200 setup time was (sec) 0.7600000 now iterating at: 11:45:42 rms-change max change #iterations 4.516681 186.1734 at 10iterations 1.991230 62.86514 at 20iterations 0.8833163 24.95715 at 30iterations 0.3920547 12.06040 at 40iterations 0.1735917 5.250745 at 50iterations 7.7267297E-02 2.385414 at 60iterations 3.4183726E-02 1.048145 at 70iterations 1.5266642E-02 0.4439650 at 80iterations 6.8231211E-03 0.2101632 at 90iterations 3.0762984E-03 8.4171295E-02 at 100iterations 1.4111662E-03 3.8108021E-02 at 110iterations 6.6910119E-04 1.9409180E-02 at 120iterations finished qdiffx linear iterations at : 11:45:50 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 6.6910119E-04 1.9409180E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.400000 DelPhi exited at 11:45:51 9.399u 0.289s 0:10.00 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 11:45:51 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4433 !!! WARNING: HIT 440 has a net charge of 0.5140 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: 2.526335 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): -27.25700 35.12900 ymin,ymax (A): 34.69100 98.10300 zmin,zma (A): 30.99300 90.89100 x,y,z range (A): 62.38600 63.41201 59.89799 scale (grids/A): 2.526335 object centre (A): 3.935999 66.39700 60.94200 number of atom coordinates read : 4433 total number of charged atoms : 4273 net assigned charge : -7.485951 assigned positive charge : 667.9782 centred at (gu) : 93.60481 83.02616 84.21929 assigned negative charge : -675.4673 centred at (gu) : 93.05366 83.28282 84.92228 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 231433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33719 grid for indexing accessible points = 1.400000 m= 113533 mr = 175632 m= 35028 mr = 93465 m= 6759 mr = 27667 m= 557 mr = 4980 m= 8 mr = 306 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 22973 time to turn everything in is 1.280000 number of dielectric boundary points 85268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 34166 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) : 1.684224 object centre at (A) : 3.935999 66.39700 60.94200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5429257 -0.2948251 midg,1,midg; midg,igrid,midg 0.2695185 -0.1186970 1,midg,midg; igrid,midg,midg -0.3558736 0.2194053 gauss-seidel spectral radius is 0.9992256 estimated iterations to convergence 284 setup time was (sec) 1.590000 now iterating at: 11:45:53 rms-change max change #iterations 11.23574 324.9161 at 10iterations 6.490573 127.7681 at 20iterations 3.732029 85.25638 at 30iterations 2.142094 38.41388 at 40iterations 1.225822 20.27965 at 50iterations 0.6996924 11.29449 at 60iterations 0.3989418 7.373863 at 70iterations 0.2272958 3.955448 at 80iterations 0.1296312 2.104682 at 90iterations 7.3655628E-02 1.408515 at 100iterations 4.1918337E-02 0.7364902 at 110iterations 2.3855114E-02 0.4066913 at 120iterations 1.3592521E-02 0.2284060 at 130iterations 7.7593587E-03 0.1254025 at 140iterations 4.4386182E-03 8.4534645E-02 at 150iterations 2.5538742E-03 4.1646957E-02 at 160iterations 1.4822072E-03 2.3792267E-02 at 170iterations 8.7375118E-04 1.4400482E-02 at 180iterations finished qdiffx linear iterations at : 11:46:07 total time elapsed so far: 15.45000 # loops : 180 mean,max change (kT/e) : 8.7375118E-04 1.4400482E-02 energy calculations done at 15.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.58000 DelPhi exited at 11:46:07 15.580u 0.297s 0:16.19 98.0% 0+0k 0+0io 0pf+0w