Mon Oct 10 22:01:37 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 22:01:37 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 = 2726 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6230530 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): -9.256000 42.76300 ymin,ymax (A): -25.42700 31.71100 zmin,zma (A): -26.19900 24.03600 x,y,z range (A): 52.01900 57.13800 50.23500 scale (grids/A): 0.6230530 object centre (A): 16.75350 3.142000 -1.081500 number of atom coordinates read : 2726 total number of charged atoms : 2638 net assigned charge : 4.000007 assigned positive charge : 412.0442 centred at (gu) : 89.00834 89.38122 90.69836 assigned negative charge : -408.0457 centred at (gu) : 88.89411 89.40263 90.70745 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7192 nv = 96 ne = 84 npr = 52914 no. pairs analyzed = 52914 no. exposed pairs = 3801 no. arc points = 26506 no. surface atoms = 1264 nbur = 1462 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 384 mr = 3635 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2648 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8808 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7184633E-09 3.3937335E-09 midg,1,midg; midg,igrid,midg 6.0039369E-09 1.7542028E-09 1,midg,midg; igrid,midg,midg -6.5439290E-09 9.8341086E-09 gauss-seidel spectral radius is 0.9866807 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 22:01:37 rms-change max change #iterations 0.1284853 21.42772 at 10iterations 1.1882095E-02 1.766843 at 20iterations 1.1733243E-03 0.1878891 at 30iterations 1.5392838E-04 1.9190788E-02 at 40iterations 3.4515531E-05 4.4422150E-03 at 50iterations finished qdiffx linear iterations at : 22:01:40 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.4515531E-05 4.4422150E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 22:01:41 3.362u 0.172s 0:04.07 86.7% 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 Mon Oct 10 2011 at 22:01:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.869159 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): -9.256000 42.76300 ymin,ymax (A): -25.42700 31.71100 zmin,zma (A): -26.19900 24.03600 x,y,z range (A): 52.01900 57.13800 50.23500 scale (grids/A): 1.869159 object centre (A): 16.75350 3.142000 -1.081500 number of atom coordinates read : 2726 total number of charged atoms : 2638 net assigned charge : 4.000007 assigned positive charge : 412.0442 centred at (gu) : 87.02424 88.14261 92.09432 assigned negative charge : -408.0457 centred at (gu) : 86.68212 88.20777 92.12214 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 77946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26506 grid for indexing accessible points = 1.400000 m= 26401 mr = 51907 m= 3999 mr = 18128 m= 184 mr = 2352 m= 5 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 36101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20643 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) : 0.6230530 object centre at (A) : 16.75350 3.142000 -1.081500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8368330E-03 4.5838426E-03 midg,1,midg; midg,igrid,midg 1.3083531E-02 1.1987667E-02 1,midg,midg; igrid,midg,midg -1.8026529E-02 1.8911935E-02 gauss-seidel spectral radius is 0.9986176 estimated iterations to convergence 213 setup time was (sec) 0.5800000 now iterating at: 22:01:42 rms-change max change #iterations 4.230293 182.3138 at 10iterations 1.968183 65.76242 at 20iterations 0.9193335 31.68496 at 30iterations 0.4289386 14.55091 at 40iterations 0.2007509 6.357222 at 50iterations 9.3875401E-02 2.999554 at 60iterations 4.3895200E-02 1.695370 at 70iterations 2.0468479E-02 0.7628021 at 80iterations 9.5264651E-03 0.3222542 at 90iterations 4.4491170E-03 0.1391075 at 100iterations 2.0760195E-03 6.8092346E-02 at 110iterations 9.7366440E-04 3.6671638E-02 at 120iterations finished qdiffx linear iterations at : 22:01:49 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 9.7366440E-04 3.6671638E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 22:01:49 7.768u 0.214s 0:08.43 94.5% 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 Mon Oct 10 2011 at 22:01:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 2.803738 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): -9.256000 42.76300 ymin,ymax (A): -25.42700 31.71100 zmin,zma (A): -26.19900 24.03600 x,y,z range (A): 52.01900 57.13800 50.23500 scale (grids/A): 2.803738 object centre (A): 16.75350 3.142000 -1.081500 number of atom coordinates read : 2726 total number of charged atoms : 2638 net assigned charge : 4.000007 assigned positive charge : 412.0442 centred at (gu) : 85.53621 87.21378 93.14120 assigned negative charge : -408.0457 centred at (gu) : 85.02324 87.31153 93.18330 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 180387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26506 grid for indexing accessible points = 1.400000 m= 85611 mr = 126614 m= 29864 mr = 67109 m= 6872 mr = 22937 m= 854 mr = 4924 m= 45 mr = 514 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.5500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 81518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 21091 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) : 1.869159 object centre at (A) : 16.75350 3.142000 -1.081500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1664959 4.2454716E-02 midg,1,midg; midg,igrid,midg 8.5971697E-04 8.7839425E-02 1,midg,midg; igrid,midg,midg -0.2689227 0.2078350 gauss-seidel spectral radius is 0.9992761 estimated iterations to convergence 293 setup time was (sec) 1.250000 now iterating at: 22:01:51 rms-change max change #iterations 10.23697 370.6805 at 10iterations 6.133701 151.6733 at 20iterations 3.629013 82.22078 at 30iterations 2.140337 50.56965 at 40iterations 1.255404 28.97542 at 50iterations 0.7328030 15.72384 at 60iterations 0.4273696 9.540056 at 70iterations 0.2492691 5.012094 at 80iterations 0.1448791 3.052661 at 90iterations 8.4072262E-02 1.624198 at 100iterations 4.8788976E-02 0.8668883 at 110iterations 2.8316306E-02 0.5225029 at 120iterations 1.6378151E-02 0.3206911 at 130iterations 9.5059248E-03 0.1666737 at 140iterations 5.5066301E-03 0.1120586 at 150iterations 3.1865698E-03 5.9806824E-02 at 160iterations 1.8462418E-03 3.3897400E-02 at 170iterations 1.0709043E-03 1.9463062E-02 at 180iterations finished qdiffx linear iterations at : 22:02:02 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.0709043E-03 1.9463062E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 22:02:03 12.974u 0.202s 0:13.91 94.6% 0+0k 0+0io 0pf+0w