Tue Oct 11 06:01:14 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 Tue Oct 11 2011 at 06:01:14 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 = 2327 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: 0.7123134 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): 25.79300 72.22800 ymin,ymax (A): -18.48600 31.49200 zmin,zma (A): 4.305000 46.54200 x,y,z range (A): 46.43500 49.97800 42.23700 scale (grids/A): 0.7123134 object centre (A): 49.01050 6.503000 25.42350 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.25758 90.12547 90.18414 assigned negative charge : -318.8441 centred at (gu) : 89.38517 90.07627 90.26861 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7276 nv = 96 ne = 84 npr = 42789 no. pairs analyzed = 42789 no. exposed pairs = 2565 no. arc points = 17596 no. surface atoms = 875 nbur = 1452 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 507 mr = 4231 m= 2 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1641 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8108 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0442008E-07 1.3404406E-08 midg,1,midg; midg,igrid,midg 3.2454849E-08 9.0715965E-08 1,midg,midg; igrid,midg,midg 1.5236972E-07 -9.6624833E-09 gauss-seidel spectral radius is 0.9897281 estimated iterations to convergence 80 setup time was (sec) 0.5300000 now iterating at: 06:01:15 rms-change max change #iterations 0.2055458 29.28913 at 10iterations 2.6333854E-02 4.151318 at 20iterations 3.4572952E-03 0.5145721 at 30iterations 5.3706043E-04 6.4754486E-02 at 40iterations 1.2349911E-04 1.6466141E-02 at 50iterations finished qdiffx linear iterations at : 06:01:18 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.2349911E-04 1.6466141E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 06:01:19 3.549u 0.178s 0:04.19 88.5% 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 Tue Oct 11 2011 at 06:01:19 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.136940 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): 25.79300 72.22800 ymin,ymax (A): -18.48600 31.49200 zmin,zma (A): 4.305000 46.54200 x,y,z range (A): 46.43500 49.97800 42.23700 scale (grids/A): 2.136940 object centre (A): 49.01050 6.503000 25.42350 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.77261 90.37623 90.55240 assigned negative charge : -318.8441 centred at (gu) : 88.15543 90.22899 90.80588 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77030 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17596 grid for indexing accessible points = 1.400000 m= 31721 mr = 54904 m= 6300 mr = 24214 m= 616 mr = 4256 m= 18 mr = 330 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 31979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15900 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) : 0.7123134 object centre at (A) : 49.01050 6.503000 25.42350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2678491E-02 2.9651009E-02 midg,1,midg; midg,igrid,midg 5.3516135E-02 2.6635583E-02 1,midg,midg; igrid,midg,midg 4.4417903E-02 -4.8314732E-02 gauss-seidel spectral radius is 0.9988480 estimated iterations to convergence 233 setup time was (sec) 0.9000000 now iterating at: 06:01:20 rms-change max change #iterations 4.660771 208.3689 at 10iterations 2.317121 73.51866 at 20iterations 1.155463 39.56647 at 30iterations 0.5758438 16.12458 at 40iterations 0.2884546 8.883238 at 50iterations 0.1437604 4.819641 at 60iterations 7.1590133E-02 2.015878 at 70iterations 3.5881802E-02 1.081158 at 80iterations 1.7895522E-02 0.5146677 at 90iterations 8.9999596E-03 0.2883549 at 100iterations 4.5217592E-03 0.1316109 at 110iterations 2.3116604E-03 7.3459625E-02 at 120iterations finished qdiffx linear iterations at : 06:01:26 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.3116604E-03 7.3459625E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 06:01:27 7.774u 0.168s 0:08.30 95.5% 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 Tue Oct 11 2011 at 06:01:27 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 = 2327 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: 3.205410 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): 25.79300 72.22800 ymin,ymax (A): -18.48600 31.49200 zmin,zma (A): 4.305000 46.54200 x,y,z range (A): 46.43500 49.97800 42.23700 scale (grids/A): 3.205410 object centre (A): 49.01050 6.503000 25.42350 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.65887 90.56425 90.82859 assigned negative charge : -318.8441 centred at (gu) : 87.23318 90.34357 91.20879 start vw surface at 0.1400000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 177886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17596 grid for indexing accessible points = 1.400000 m= 97951 mr = 132381 m= 40760 mr = 81860 m= 11951 mr = 33658 m= 2520 mr = 9463 m= 293 mr = 1809 m= 20 mr = 205 m= 0 mr = 7 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.930000 number of dielectric boundary points 71998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 16016 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) : 2.136940 object centre at (A) : 49.01050 6.503000 25.42350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1178304 0.2369749 midg,1,midg; midg,igrid,midg 0.4285452 0.1199480 1,midg,midg; igrid,midg,midg 0.4282083 -0.6049471 gauss-seidel spectral radius is 0.9993008 estimated iterations to convergence 298 setup time was (sec) 2.240000 now iterating at: 06:01:29 rms-change max change #iterations 10.41873 375.4194 at 10iterations 6.159997 123.7333 at 20iterations 3.646500 72.91237 at 30iterations 2.152913 39.46207 at 40iterations 1.268734 27.56483 at 50iterations 0.7452927 14.90370 at 60iterations 0.4382080 7.459915 at 70iterations 0.2575110 4.375896 at 80iterations 0.1510811 2.639747 at 90iterations 8.8694252E-02 1.535891 at 100iterations 5.2002832E-02 0.9437866 at 110iterations 3.0653059E-02 0.5178032 at 120iterations 1.8101014E-02 0.3102999 at 130iterations 1.0802253E-02 0.2017851 at 140iterations 6.5490901E-03 0.1140690 at 150iterations 4.0624333E-03 7.0556641E-02 at 160iterations 2.6318568E-03 4.9263000E-02 at 170iterations 1.8009098E-03 3.2367706E-02 at 180iterations finished qdiffx linear iterations at : 06:01:40 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 1.8009098E-03 3.2367706E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 06:01:41 13.429u 0.210s 0:14.20 95.9% 0+0k 0+0io 0pf+0w