Tue Oct 11 07:00:25 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+sph2.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 = amb2.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 07:00:25 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2949 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5438603 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): -19.82000 45.63800 ymin,ymax (A): 21.55300 78.38300 zmin,zma (A): -71.55800 -23.74900 x,y,z range (A): 65.45799 56.83000 47.80900 scale (grids/A): 0.5438603 object centre (A): 12.90900 49.96800 -47.65350 number of atom coordinates read : 2949 total number of charged atoms : 2806 net assigned charge : -1.960990 assigned positive charge : 431.1475 centred at (gu) : 89.30430 89.86045 89.78018 assigned negative charge : -433.1092 centred at (gu) : 89.30540 89.95187 89.79555 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5734 nv = 96 ne = 84 npr = 60141 no. pairs analyzed = 60141 no. exposed pairs = 3676 no. arc points = 25987 no. surface atoms = 1233 nbur = 1716 mkacc time = 0.2000000 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 = 3039 m= 0 mr = 14 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 2909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2582 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7400 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2442041E-11 -1.9449793E-10 midg,1,midg; midg,igrid,midg 4.4283213E-10 -6.4349703E-10 1,midg,midg; igrid,midg,midg -1.2610149E-10 -1.0137223E-10 gauss-seidel spectral radius is 0.9825711 estimated iterations to convergence 62 setup time was (sec) 0.7000000 now iterating at: 07:00:26 rms-change max change #iterations 7.1715109E-02 13.18001 at 10iterations 4.8210640E-03 0.7753665 at 20iterations 3.6164763E-04 6.8382263E-02 at 30iterations 4.5087254E-05 1.2182236E-02 at 40iterations 9.3294721E-06 2.7046204E-03 at 50iterations finished qdiffx linear iterations at : 07:00:30 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 9.3294721E-06 2.7046204E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.830000 DelPhi exited at 07:00:30 4.834u 0.446s 0:05.60 94.1% 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 07:00:30 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2949 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.631581 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): -19.82000 45.63800 ymin,ymax (A): 21.55300 78.38300 zmin,zma (A): -71.55800 -23.74900 x,y,z range (A): 65.45799 56.83000 47.80900 scale (grids/A): 1.631581 object centre (A): 12.90900 49.96800 -47.65350 number of atom coordinates read : 2949 total number of charged atoms : 2806 net assigned charge : -1.960990 assigned positive charge : 431.1475 centred at (gu) : 87.91209 89.58079 89.34013 assigned negative charge : -433.1092 centred at (gu) : 87.91573 89.85506 89.38623 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 62817 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25987 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20994 mr = 42616 m= 2550 mr = 15135 m= 55 mr = 1490 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 0.6500000 number of dielectric boundary points 27173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 300 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 21530 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) : 0.5438603 object centre at (A) : 12.90900 49.96800 -47.65350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2560413E-03 6.6241263E-03 midg,1,midg; midg,igrid,midg -2.7456712E-03 3.4939116E-03 1,midg,midg; igrid,midg,midg -1.4078016E-04 -2.4990587E-02 gauss-seidel spectral radius is 0.9981847 estimated iterations to convergence 186 setup time was (sec) 1.040000 now iterating at: 07:00:32 rms-change max change #iterations 3.268799 153.2069 at 10iterations 1.357843 54.86842 at 20iterations 0.5677467 25.02188 at 30iterations 0.2370002 8.587188 at 40iterations 9.8792277E-02 3.617386 at 50iterations 4.1267756E-02 1.605984 at 60iterations 1.7229356E-02 0.6478872 at 70iterations 7.1902517E-03 0.2806797 at 80iterations 3.0067340E-03 0.1058121 at 90iterations 1.2643429E-03 4.7496557E-02 at 100iterations 5.3048279E-04 1.8305779E-02 at 110iterations 2.2639663E-04 8.0585480E-03 at 120iterations finished qdiffx linear iterations at : 07:00:42 total time elapsed so far: 10.67000 # loops : 120 mean,max change (kT/e) : 2.2639663E-04 8.0585480E-03 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.88000 DelPhi exited at 07:00:42 10.883u 0.511s 0:11.86 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 07:00:42 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2949 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.447371 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): -19.82000 45.63800 ymin,ymax (A): 21.55300 78.38300 zmin,zma (A): -71.55800 -23.74900 x,y,z range (A): 65.45799 56.83000 47.80900 scale (grids/A): 2.447371 object centre (A): 12.90900 49.96800 -47.65350 number of atom coordinates read : 2949 total number of charged atoms : 2806 net assigned charge : -1.960990 assigned positive charge : 431.1475 centred at (gu) : 86.86800 89.37111 89.01006 assigned negative charge : -433.1092 centred at (gu) : 86.87358 89.78252 89.07928 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 145501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25987 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 70454 mr = 103828 m= 22250 mr = 56702 m= 4162 mr = 17575 m= 316 mr = 3103 m= 5 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 2024 time to turn everything in is 1.670000 number of dielectric boundary points 61316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 22423 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) : 1.631581 object centre at (A) : 12.90900 49.96800 -47.65350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4653687E-02 0.1231354 midg,1,midg; midg,igrid,midg -3.2114342E-02 8.0719419E-02 1,midg,midg; igrid,midg,midg -6.2325552E-02 -0.6805745 gauss-seidel spectral radius is 0.9991382 estimated iterations to convergence 269 setup time was (sec) 2.040000 now iterating at: 07:00:45 rms-change max change #iterations 8.433802 276.0353 at 10iterations 4.705040 115.1061 at 20iterations 2.625722 65.50763 at 30iterations 1.460793 33.27051 at 40iterations 0.8074089 19.02056 at 50iterations 0.4456133 9.497803 at 60iterations 0.2463049 5.011541 at 70iterations 0.1356200 2.827424 at 80iterations 7.4748687E-02 1.530804 at 90iterations 4.1101731E-02 0.8143263 at 100iterations 2.2566063E-02 0.4770050 at 110iterations 1.2436590E-02 0.2550659 at 120iterations 6.8232263E-03 0.1310105 at 130iterations 3.7490199E-03 7.4428558E-02 at 140iterations 2.0636744E-03 4.2959213E-02 at 150iterations 1.1356013E-03 2.7889252E-02 at 160iterations 6.2363828E-04 1.3306260E-02 at 170iterations 3.4272083E-04 7.1308902E-03 at 180iterations finished qdiffx linear iterations at : 07:01:01 total time elapsed so far: 18.02000 # loops : 180 mean,max change (kT/e) : 3.4272083E-04 7.1308902E-03 energy calculations done at 18.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.23000 DelPhi exited at 07:01:02 18.234u 0.472s 0:19.33 96.7% 0+0k 0+0io 0pf+0w