Tue Oct 11 08:29:06 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 08:29:06 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 = 3173 !!! WARNING: ASP 161 has a net charge of -0.2720 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: 0.5418734 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): -23.18400 41.53600 ymin,ymax (A): -3.834000 42.73500 zmin,zma (A): 32.98900 98.68700 x,y,z range (A): 64.72000 46.56900 65.69801 scale (grids/A): 0.5418734 object centre (A): 9.176002 19.45050 65.83800 number of atom coordinates read : 3173 total number of charged atoms : 3035 net assigned charge : -5.271970 assigned positive charge : 473.0798 centred at (gu) : 89.40671 89.61709 92.65086 assigned negative charge : -478.3528 centred at (gu) : 89.41124 89.66113 92.74352 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5892 nv = 96 ne = 84 npr = 66361 no. pairs analyzed = 66361 no. exposed pairs = 3695 no. arc points = 26029 no. surface atoms = 1259 nbur = 1914 mkacc time = 0.1100000 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 = 1.596000 m= 228 mr = 3163 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2819 ## 421 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7941 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4765283E-10 -1.6253565E-09 midg,1,midg; midg,igrid,midg 6.5149188E-12 -4.8164961E-10 1,midg,midg; igrid,midg,midg -2.6919322E-10 -2.4988547E-10 gauss-seidel spectral radius is 0.9824532 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 08:29:07 rms-change max change #iterations 7.4108735E-02 12.02115 at 10iterations 4.7636237E-03 0.7790413 at 20iterations 3.2512497E-04 5.3497553E-02 at 30iterations 3.0873638E-05 5.6703091E-03 at 40iterations 5.8869109E-06 1.3890266E-03 at 50iterations finished qdiffx linear iterations at : 08:29:09 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 5.8869109E-06 1.3890266E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 08:29:10 3.501u 0.159s 0:04.05 90.1% 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 08:29:10 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 = 3173 !!! WARNING: ASP 161 has a net charge of -0.2720 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: 1.625620 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): -23.18400 41.53600 ymin,ymax (A): -3.834000 42.73500 zmin,zma (A): 32.98900 98.68700 x,y,z range (A): 64.72000 46.56900 65.69801 scale (grids/A): 1.625620 object centre (A): 9.176002 19.45050 65.83800 number of atom coordinates read : 3173 total number of charged atoms : 3035 net assigned charge : -5.271970 assigned positive charge : 473.0798 centred at (gu) : 88.21928 88.85055 97.95172 assigned negative charge : -478.3528 centred at (gu) : 88.23342 88.98282 98.23009 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65658 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21058 mr = 45387 m= 2092 mr = 15095 m= 63 mr = 1071 m= 0 mr = 7 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1354 time to turn everything in is 0.3300000 number of dielectric boundary points 27311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 344 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 23167 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) : 0.5418734 object centre at (A) : 9.176002 19.45050 65.83800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9277329E-02 -1.9289168E-02 midg,1,midg; midg,igrid,midg -1.3829488E-03 -5.3001442E-03 1,midg,midg; igrid,midg,midg -1.7627459E-02 -1.3569787E-02 gauss-seidel spectral radius is 0.9981719 estimated iterations to convergence 186 setup time was (sec) 0.5400000 now iterating at: 08:29:11 rms-change max change #iterations 3.356985 144.7078 at 10iterations 1.391248 50.34059 at 20iterations 0.5781476 23.24817 at 30iterations 0.2412869 9.105064 at 40iterations 0.1001268 3.379657 at 50iterations 4.1548442E-02 1.452484 at 60iterations 1.7384186E-02 0.6097221 at 70iterations 7.1988995E-03 0.2508316 at 80iterations 3.0157492E-03 0.1117420 at 90iterations 1.2533868E-03 4.3026924E-02 at 100iterations 5.2387320E-04 1.9900322E-02 at 110iterations 2.1906871E-04 8.8310242E-03 at 120iterations finished qdiffx linear iterations at : 08:29:19 total time elapsed so far: 8.450000 # loops : 120 mean,max change (kT/e) : 2.1906871E-04 8.8310242E-03 energy calculations done at 8.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 08:29:19 8.586u 0.213s 0:09.15 96.0% 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 08:29:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3173 !!! WARNING: ASP 161 has a net charge of -0.2720 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: 2.438430 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): -23.18400 41.53600 ymin,ymax (A): -3.834000 42.73500 zmin,zma (A): 32.98900 98.68700 x,y,z range (A): 64.72000 46.56900 65.69801 scale (grids/A): 2.438430 object centre (A): 9.176002 19.45050 65.83800 number of atom coordinates read : 3173 total number of charged atoms : 3035 net assigned charge : -5.271970 assigned positive charge : 473.0798 centred at (gu) : 87.32890 88.27559 101.9273 assigned negative charge : -478.3528 centred at (gu) : 87.35007 88.47424 102.3450 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 72852 mr = 110822 m= 21204 mr = 58998 m= 3342 mr = 16347 m= 272 mr = 2162 m= 5 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 4577 time to turn everything in is 0.8000000 number of dielectric boundary points 61759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24245 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) : 1.625620 object centre at (A) : 9.176002 19.45050 65.83800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2085493 -0.1111848 midg,1,midg; midg,igrid,midg -1.4507861E-02 -7.0947364E-02 1,midg,midg; igrid,midg,midg -0.3361170 -0.2740301 gauss-seidel spectral radius is 0.9991328 estimated iterations to convergence 268 setup time was (sec) 1.030000 now iterating at: 08:29:20 rms-change max change #iterations 8.652528 281.4837 at 10iterations 4.797969 115.7077 at 20iterations 2.660119 60.74754 at 30iterations 1.464518 33.45911 at 40iterations 0.8104386 16.24607 at 50iterations 0.4460606 9.878443 at 60iterations 0.2450425 5.079032 at 70iterations 0.1343940 2.716689 at 80iterations 7.3820278E-02 1.440691 at 90iterations 4.0517256E-02 0.8507957 at 100iterations 2.2246713E-02 0.4804883 at 110iterations 1.2165689E-02 0.2589359 at 120iterations 6.6836346E-03 0.1372375 at 130iterations 3.6655413E-03 7.9299927E-02 at 140iterations 2.0121853E-03 3.9963961E-02 at 150iterations 1.1036783E-03 2.1348953E-02 at 160iterations 6.0485303E-04 1.3022423E-02 at 170iterations 3.3152220E-04 7.2698593E-03 at 180iterations finished qdiffx linear iterations at : 08:29:31 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 3.3152220E-04 7.2698593E-03 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 08:29:32 11.982u 0.194s 0:12.56 96.8% 0+0k 0+0io 0pf+0w