Mon Oct 10 09:09:44 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 09:09:44 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 = 1970 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: 0.6250548 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): -35.24400 10.60100 ymin,ymax (A): 0.3510000 42.82100 zmin,zma (A): -0.6590000 56.29600 x,y,z range (A): 45.84501 42.47000 56.95500 scale (grids/A): 0.6250548 object centre (A): -12.32150 21.58600 27.81850 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 287.8740 centred at (gu) : 90.20601 89.36240 90.04541 assigned negative charge : -284.8743 centred at (gu) : 90.13829 89.53634 90.04705 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5249 nv = 96 ne = 84 npr = 40234 no. pairs analyzed = 40234 no. exposed pairs = 2505 no. arc points = 17229 no. surface atoms = 850 nbur = 1120 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 247 mr = 2890 m= 0 mr = 32 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1789 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6258 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8124101E-09 2.6797602E-09 midg,1,midg; midg,igrid,midg 1.4253780E-08 -6.2883689E-09 1,midg,midg; igrid,midg,midg -1.0496640E-09 6.8424262E-09 gauss-seidel spectral radius is 0.9866897 estimated iterations to convergence 71 setup time was (sec) 0.3600000 now iterating at: 09:09:45 rms-change max change #iterations 0.1087791 21.74368 at 10iterations 1.0218649E-02 1.692930 at 20iterations 9.6032233E-04 0.1831102 at 30iterations 8.9391135E-05 1.5430212E-02 at 40iterations 8.2764318E-06 1.2702942E-03 at 50iterations finished qdiffx linear iterations at : 09:09:48 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 8.2764318E-06 1.2702942E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 09:09:48 3.413u 0.434s 0:04.25 90.3% 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 09:09:48 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 = 1970 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: 1.875165 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): -35.24400 10.60100 ymin,ymax (A): 0.3510000 42.82100 zmin,zma (A): -0.6590000 56.29600 x,y,z range (A): 45.84501 42.47000 56.95500 scale (grids/A): 1.875165 object centre (A): -12.32150 21.58600 27.81850 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 287.8740 centred at (gu) : 90.61808 88.08698 90.13595 assigned negative charge : -284.8743 centred at (gu) : 90.41528 88.60921 90.14117 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 56194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17229 grid for indexing accessible points = 1.400000 m= 20939 mr = 38527 m= 3312 mr = 15823 m= 191 mr = 2214 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 23990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14431 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) : 0.6250548 object centre at (A) : -12.32150 21.58600 27.81850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1557424E-02 2.5233969E-02 midg,1,midg; midg,igrid,midg 8.1093404E-03 -8.0307638E-03 1,midg,midg; igrid,midg,midg -3.8673577E-03 -3.6757330E-03 gauss-seidel spectral radius is 0.9985182 estimated iterations to convergence 206 setup time was (sec) 0.5200000 now iterating at: 09:09:49 rms-change max change #iterations 3.423636 164.9948 at 10iterations 1.561921 60.46353 at 20iterations 0.7057320 25.44716 at 30iterations 0.3206210 11.27188 at 40iterations 0.1453830 5.544477 at 50iterations 6.5903679E-02 2.583834 at 60iterations 2.9906020E-02 1.172478 at 70iterations 1.3541966E-02 0.4933014 at 80iterations 6.1585172E-03 0.2369461 at 90iterations 2.7921335E-03 0.1036301 at 100iterations 1.2614335E-03 4.7004938E-02 at 110iterations 5.7257025E-04 1.9969940E-02 at 120iterations finished qdiffx linear iterations at : 09:09:57 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 5.7257025E-04 1.9969940E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.420000 DelPhi exited at 09:09:57 8.418u 0.239s 0:09.06 95.3% 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 09:09:57 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 = 1970 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: 2.812747 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): -35.24400 10.60100 ymin,ymax (A): 0.3510000 42.82100 zmin,zma (A): -0.6590000 56.29600 x,y,z range (A): 45.84501 42.47000 56.95500 scale (grids/A): 2.812747 object centre (A): -12.32150 21.58600 27.81850 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 287.8740 centred at (gu) : 90.92715 87.13057 90.20403 assigned negative charge : -284.8743 centred at (gu) : 90.62289 87.91386 90.21188 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 129521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17229 grid for indexing accessible points = 1.400000 m= 67161 mr = 92851 m= 25254 mr = 55635 m= 6051 mr = 20925 m= 820 mr = 4749 m= 55 mr = 605 m= 0 mr = 31 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 54066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 14704 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) : 1.875165 object centre at (A) : -12.32150 21.58600 27.81850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4068578E-02 0.1147844 midg,1,midg; midg,igrid,midg 1.6140310E-02 -9.4248712E-02 1,midg,midg; igrid,midg,midg -7.3493943E-02 -7.0465900E-02 gauss-seidel spectral radius is 0.9992101 estimated iterations to convergence 281 setup time was (sec) 0.9700000 now iterating at: 09:09:59 rms-change max change #iterations 8.159929 345.0837 at 10iterations 4.673025 120.5250 at 20iterations 2.649139 63.65216 at 30iterations 1.500082 32.42737 at 40iterations 0.8464773 17.87293 at 50iterations 0.4779974 9.806995 at 60iterations 0.2689286 5.326999 at 70iterations 0.1515422 2.994370 at 80iterations 8.5455187E-02 1.762753 at 90iterations 4.8023064E-02 0.9899321 at 100iterations 2.7065268E-02 0.5564728 at 110iterations 1.5152918E-02 0.3148880 at 120iterations 8.5623749E-03 0.1764774 at 130iterations 4.8247003E-03 9.5458984E-02 at 140iterations 2.7076653E-03 6.0619354E-02 at 150iterations 1.5259840E-03 3.1453133E-02 at 160iterations 8.5893739E-04 1.7546654E-02 at 170iterations 4.8291785E-04 9.7351074E-03 at 180iterations finished qdiffx linear iterations at : 09:10:10 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 4.8291785E-04 9.7351074E-03 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 09:10:10 12.219u 0.236s 0:12.91 96.3% 0+0k 0+0io 0pf+0w