Mon Oct 10 14:11:07 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 Mon Oct 10 2011 at 14:11:07 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 = 2623 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6219102 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): 16.77400 74.01700 ymin,ymax (A): 12.92000 63.31900 zmin,zma (A): 20.06800 64.70500 x,y,z range (A): 57.24300 50.39900 44.63700 scale (grids/A): 0.6219102 object centre (A): 45.39550 38.11950 42.38650 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : -0.9999961 assigned positive charge : 401.2148 centred at (gu) : 90.37452 91.57731 91.45277 assigned negative charge : -402.2154 centred at (gu) : 90.41338 91.36372 91.53394 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6699 nv = 96 ne = 84 npr = 52575 no. pairs analyzed = 52575 no. exposed pairs = 3239 no. arc points = 23627 no. surface atoms = 1090 nbur = 1533 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3528 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.3000000 number of dielectric boundary points 3487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2385 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8231 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4919625E-09 -9.6027586E-09 midg,1,midg; midg,igrid,midg -1.1880166E-08 2.0184219E-08 1,midg,midg; igrid,midg,midg 1.6609023E-09 -4.1530956E-09 gauss-seidel spectral radius is 0.9866152 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 14:11:08 rms-change max change #iterations 0.1286786 18.50892 at 10iterations 1.1872256E-02 1.743614 at 20iterations 1.1014625E-03 0.1719007 at 30iterations 1.0189821E-04 1.7791748E-02 at 40iterations 9.2645405E-06 1.3391972E-03 at 50iterations finished qdiffx linear iterations at : 14:11:12 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 9.2645405E-06 1.3391972E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 14:11:12 4.472u 0.414s 0:05.19 94.0% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 14:11:12 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 = 2623 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.865730 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): 16.77400 74.01700 ymin,ymax (A): 12.92000 63.31900 zmin,zma (A): 20.06800 64.70500 x,y,z range (A): 57.24300 50.39900 44.63700 scale (grids/A): 1.865730 object centre (A): 45.39550 38.11950 42.38650 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : -0.9999961 assigned positive charge : 401.2148 centred at (gu) : 91.12296 94.73167 94.35767 assigned negative charge : -402.2154 centred at (gu) : 91.24010 94.09078 94.60134 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72424 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23627 grid for indexing accessible points = 1.400000 m= 23909 mr = 48769 m= 3450 mr = 17037 m= 178 mr = 2042 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1402 time to turn everything in is 0.5700000 number of dielectric boundary points 32061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19473 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) : 0.6219102 object centre at (A) : 45.39550 38.11950 42.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7048787E-03 -1.5793711E-02 midg,1,midg; midg,igrid,midg -1.6473338E-02 1.4888886E-02 1,midg,midg; igrid,midg,midg 8.9548370E-03 -2.3696784E-02 gauss-seidel spectral radius is 0.9985843 estimated iterations to convergence 211 setup time was (sec) 0.8800000 now iterating at: 14:11:14 rms-change max change #iterations 4.100394 164.5538 at 10iterations 1.891848 71.16809 at 20iterations 0.8694661 30.22385 at 30iterations 0.3987113 14.24747 at 40iterations 0.1849646 6.611435 at 50iterations 8.5209198E-02 2.552704 at 60iterations 3.9330218E-02 1.204813 at 70iterations 1.8144641E-02 0.5775452 at 80iterations 8.3606411E-03 0.3118935 at 90iterations 3.8591307E-03 0.1268730 at 100iterations 1.7759252E-03 6.2591553E-02 at 110iterations 8.2417054E-04 2.6875973E-02 at 120iterations finished qdiffx linear iterations at : 14:11:24 total time elapsed so far: 10.89000 # loops : 120 mean,max change (kT/e) : 8.2417054E-04 2.6875973E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 14:11:24 11.062u 0.433s 0:11.92 96.3% 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 Mon Oct 10 2011 at 14:11:24 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 = 2623 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.798596 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): 16.77400 74.01700 ymin,ymax (A): 12.92000 63.31900 zmin,zma (A): 20.06800 64.70500 x,y,z range (A): 57.24300 50.39900 44.63700 scale (grids/A): 2.798596 object centre (A): 45.39550 38.11950 42.38650 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : -0.9999961 assigned positive charge : 401.2148 centred at (gu) : 91.68436 97.09724 96.53631 assigned negative charge : -402.2154 centred at (gu) : 91.85992 96.13609 96.90192 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 168213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23627 grid for indexing accessible points = 1.400000 m= 78913 mr = 119112 m= 26298 mr = 63474 m= 5927 mr = 20522 m= 811 mr = 4301 m= 42 mr = 523 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 4559 time to turn everything in is 1.490000 number of dielectric boundary points 72269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 19860 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) : 1.865730 object centre at (A) : 45.39550 38.11950 42.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5162179E-02 -0.3153225 midg,1,midg; midg,igrid,midg -0.1380835 0.1429355 1,midg,midg; igrid,midg,midg 0.1854549 -0.1503554 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.820000 now iterating at: 14:11:26 rms-change max change #iterations 9.765887 474.3744 at 10iterations 5.652915 126.5948 at 20iterations 3.249683 65.79909 at 30iterations 1.859983 39.62541 at 40iterations 1.063193 21.44361 at 50iterations 0.6071285 10.63134 at 60iterations 0.3457052 6.973932 at 70iterations 0.1973161 3.670411 at 80iterations 0.1125931 2.001595 at 90iterations 6.4075112E-02 1.149902 at 100iterations 3.6417868E-02 0.6736517 at 110iterations 2.0749101E-02 0.3995609 at 120iterations 1.1880121E-02 0.2289391 at 130iterations 6.7676855E-03 0.1321163 at 140iterations 3.8477601E-03 7.0501328E-02 at 150iterations 2.1902134E-03 4.0155411E-02 at 160iterations 1.2508042E-03 2.2727348E-02 at 170iterations 7.1278081E-04 1.2809753E-02 at 180iterations finished qdiffx linear iterations at : 14:11:43 total time elapsed so far: 18.44000 # loops : 180 mean,max change (kT/e) : 7.1278081E-04 1.2809753E-02 energy calculations done at 18.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.61000 DelPhi exited at 14:11:44 18.617u 0.477s 0:19.56 97.5% 0+0k 0+0io 0pf+0w