Sat Oct 15 11:28:24 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 Sat Oct 15 2011 at 11:28:24 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 = 3600 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: 0.5140126 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): -5.143000 64.11600 ymin,ymax (A): 14.51300 76.14900 zmin,zma (A): -13.38600 34.62200 x,y,z range (A): 69.25900 61.63600 48.00800 scale (grids/A): 0.5140126 object centre (A): 29.48650 45.33100 10.61800 number of atom coordinates read : 3600 total number of charged atoms : 3453 net assigned charge : -7.999989 assigned positive charge : 544.4220 centred at (gu) : 90.04015 87.47775 89.49886 assigned negative charge : -552.4238 centred at (gu) : 90.02077 87.51668 89.52710 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5946 nv = 96 ne = 84 npr = 73274 no. pairs analyzed = 73274 no. exposed pairs = 4355 no. arc points = 30408 no. surface atoms = 1468 nbur = 2132 mkacc time = 0.1300000 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 = 1.652000 m= 220 mr = 3123 m= 1 mr = 3 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 0.2400000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2994 ## 428 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.8176687E-11 -1.7499693E-10 midg,1,midg; midg,igrid,midg -8.0811635E-11 -1.1759639E-10 1,midg,midg; igrid,midg,midg -1.7674338E-10 -9.0325476E-11 gauss-seidel spectral radius is 0.9805527 estimated iterations to convergence 59 setup time was (sec) 0.4300000 now iterating at: 11:28:25 rms-change max change #iterations 5.8933780E-02 13.30394 at 10iterations 3.3875646E-03 0.5467529 at 20iterations 2.2758573E-04 3.9186478E-02 at 30iterations 2.8093629E-05 5.2986145E-03 at 40iterations 5.5859414E-06 1.1005402E-03 at 50iterations finished qdiffx linear iterations at : 11:28:28 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 5.5859414E-06 1.1005402E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 11:28:28 3.461u 0.186s 0:03.92 92.8% 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 15 2011 at 11:28:28 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 = 3600 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: 1.542038 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): -5.143000 64.11600 ymin,ymax (A): 14.51300 76.14900 zmin,zma (A): -13.38600 34.62200 x,y,z range (A): 69.25900 61.63600 48.00800 scale (grids/A): 1.542038 object centre (A): 29.48650 45.33100 10.61800 number of atom coordinates read : 3600 total number of charged atoms : 3453 net assigned charge : -7.999989 assigned positive charge : 544.4220 centred at (gu) : 90.11946 82.43228 88.49552 assigned negative charge : -552.4238 centred at (gu) : 90.06160 82.54948 88.58113 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 67292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19628 mr = 46356 m= 1822 mr = 13391 m= 35 mr = 833 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 414 time to turn everything in is 0.3400000 number of dielectric boundary points 28197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 409 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 26080 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) : 0.5140126 object centre at (A) : 29.48650 45.33100 10.61800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5889489E-04 -1.7576760E-03 midg,1,midg; midg,igrid,midg -1.5737772E-02 -1.3099028E-02 1,midg,midg; igrid,midg,midg 6.3693658E-03 -3.8579272E-03 gauss-seidel spectral radius is 0.9980035 estimated iterations to convergence 178 setup time was (sec) 0.5700000 now iterating at: 11:28:29 rms-change max change #iterations 3.256108 154.5718 at 10iterations 1.298744 51.88335 at 20iterations 0.5217606 18.38520 at 30iterations 0.2083933 7.828883 at 40iterations 8.3143778E-02 3.025360 at 50iterations 3.3399895E-02 1.114647 at 60iterations 1.3390149E-02 0.5120134 at 70iterations 5.3623077E-03 0.1995564 at 80iterations 2.1443150E-03 7.4366093E-02 at 90iterations 8.6417521E-04 3.2172441E-02 at 100iterations 3.4953895E-04 1.2680054E-02 at 110iterations 1.4305318E-04 4.8847198E-03 at 120iterations finished qdiffx linear iterations at : 11:28:36 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.4305318E-04 4.8847198E-03 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 11:28:36 7.730u 0.192s 0:08.27 95.7% 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 15 2011 at 11:28:36 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 = 3600 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: 2.313057 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): -5.143000 64.11600 ymin,ymax (A): 14.51300 76.14900 zmin,zma (A): -13.38600 34.62200 x,y,z range (A): 69.25900 61.63600 48.00800 scale (grids/A): 2.313057 object centre (A): 29.48650 45.33100 10.61800 number of atom coordinates read : 3600 total number of charged atoms : 3453 net assigned charge : -7.999989 assigned positive charge : 544.4220 centred at (gu) : 90.17890 78.64808 87.74327 assigned negative charge : -552.4238 centred at (gu) : 90.09247 78.82415 87.87159 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 156841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70418 mr = 113969 m= 18177 mr = 55448 m= 2649 mr = 13363 m= 123 mr = 1689 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1368 time to turn everything in is 0.8000000 number of dielectric boundary points 63709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 27546 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) : 1.542038 object centre at (A) : 29.48650 45.33100 10.61800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1228834E-02 -1.8435303E-02 midg,1,midg; midg,igrid,midg -0.3161854 -0.2524267 1,midg,midg; igrid,midg,midg 0.3798712 -6.2141202E-02 gauss-seidel spectral radius is 0.9990849 estimated iterations to convergence 261 setup time was (sec) 1.040000 now iterating at: 11:28:38 rms-change max change #iterations 8.743006 247.5265 at 10iterations 4.838891 121.7580 at 20iterations 2.653121 64.71194 at 30iterations 1.451802 35.48913 at 40iterations 0.7916136 21.77123 at 50iterations 0.4307750 9.402430 at 60iterations 0.2336272 5.327850 at 70iterations 0.1268454 2.522223 at 80iterations 6.8485357E-02 1.582219 at 90iterations 3.7110206E-02 0.7397871 at 100iterations 2.0046683E-02 0.4215086 at 110iterations 1.0857131E-02 0.2166462 at 120iterations 5.8651166E-03 0.1287212 at 130iterations 3.1817576E-03 6.7834377E-02 at 140iterations 1.7305027E-03 3.5446167E-02 at 150iterations 9.4826543E-04 2.0993233E-02 at 160iterations 5.2701595E-04 1.1725426E-02 at 170iterations 2.9938627E-04 7.9360008E-03 at 180iterations finished qdiffx linear iterations at : 11:28:49 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 2.9938627E-04 7.9360008E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 11:28:50 12.417u 0.243s 0:13.35 94.7% 0+0k 0+0io 0pf+0w