Sat Oct 8 23:09:25 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 Sat Oct 8 2011 at 23:09:25 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 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: 0.6471080 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): -13.83800 41.17600 ymin,ymax (A): 12.44900 65.45600 zmin,zma (A): 3.136000 45.66000 x,y,z range (A): 55.01400 53.00700 42.52400 scale (grids/A): 0.6471080 object centre (A): 13.66900 38.95250 24.39800 number of atom coordinates read : 2423 total number of charged atoms : 2287 net assigned charge : 12.00002 assigned positive charge : 355.6472 centred at (gu) : 89.92914 88.99445 89.11533 assigned negative charge : -343.6480 centred at (gu) : 89.97516 88.98810 89.20164 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6973 nv = 96 ne = 84 npr = 48564 no. pairs analyzed = 48564 no. exposed pairs = 3117 no. arc points = 22461 no. surface atoms = 1044 nbur = 1379 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3742 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2900000 number of dielectric boundary points 3585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2113 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8430347E-08 8.7535996E-09 midg,1,midg; midg,igrid,midg 2.5137338E-08 1.7963160E-08 1,midg,midg; igrid,midg,midg 2.7367951E-08 1.5253157E-08 gauss-seidel spectral radius is 0.9876173 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 23:09:26 rms-change max change #iterations 0.1445218 26.41181 at 10iterations 1.4562694E-02 1.841818 at 20iterations 1.6064794E-03 0.2665215 at 30iterations 2.6953165E-04 4.7358513E-02 at 40iterations 7.6425378E-05 1.5991211E-02 at 50iterations finished qdiffx linear iterations at : 23:09:30 total time elapsed so far: 4.440000 # loops : 50 mean,max change (kT/e) : 7.6425378E-05 1.5991211E-02 energy calculations done at 4.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 23:09:30 4.617u 0.369s 0:05.25 94.6% 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 8 2011 at 23:09:31 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 = 2423 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: 1.941324 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): -13.83800 41.17600 ymin,ymax (A): 12.44900 65.45600 zmin,zma (A): 3.136000 45.66000 x,y,z range (A): 55.01400 53.00700 42.52400 scale (grids/A): 1.941324 object centre (A): 13.66900 38.95250 24.39800 number of atom coordinates read : 2423 total number of charged atoms : 2287 net assigned charge : 12.00002 assigned positive charge : 355.6472 centred at (gu) : 89.78690 86.98328 87.34576 assigned negative charge : -343.6480 centred at (gu) : 89.92558 86.96420 87.60490 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 73596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22461 grid for indexing accessible points = 1.400000 m= 27450 mr = 49739 m= 5347 mr = 20139 m= 458 mr = 3537 m= 12 mr = 224 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.6000000 number of dielectric boundary points 33224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18020 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) : 0.6471080 object centre at (A) : 13.66900 38.95250 24.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6975082E-02 1.2203953E-03 midg,1,midg; midg,igrid,midg 2.5583714E-02 5.6228515E-02 1,midg,midg; igrid,midg,midg 5.9042033E-02 1.5735537E-02 gauss-seidel spectral radius is 0.9986755 estimated iterations to convergence 218 setup time was (sec) 0.9200000 now iterating at: 23:09:32 rms-change max change #iterations 4.132864 193.3468 at 10iterations 1.952111 77.65846 at 20iterations 0.9252386 30.30183 at 30iterations 0.4358461 14.40675 at 40iterations 0.2063715 8.107834 at 50iterations 9.8241836E-02 3.135048 at 60iterations 4.6360265E-02 1.449414 at 70iterations 2.1936558E-02 0.6949463 at 80iterations 1.0430343E-02 0.3486023 at 90iterations 4.9982495E-03 0.1616077 at 100iterations 2.4076556E-03 7.8023911E-02 at 110iterations 1.1904050E-03 4.0880442E-02 at 120iterations finished qdiffx linear iterations at : 23:09:42 total time elapsed so far: 11.48000 # loops : 120 mean,max change (kT/e) : 1.1904050E-03 4.0880442E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.64000 DelPhi exited at 23:09:43 11.647u 0.438s 0:12.36 97.6% 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 8 2011 at 23:09:43 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 = 2423 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: 2.911986 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): -13.83800 41.17600 ymin,ymax (A): 12.44900 65.45600 zmin,zma (A): 3.136000 45.66000 x,y,z range (A): 55.01400 53.00700 42.52400 scale (grids/A): 2.911986 object centre (A): 13.66900 38.95250 24.39800 number of atom coordinates read : 2423 total number of charged atoms : 2287 net assigned charge : 12.00002 assigned positive charge : 355.6472 centred at (gu) : 89.68021 85.47470 86.01852 assigned negative charge : -343.6480 centred at (gu) : 89.88840 85.44631 86.40744 start vw surface at 0.1100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 169784 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22461 grid for indexing accessible points = 1.400000 m= 86218 mr = 120728 m= 34396 mr = 69813 m= 10184 mr = 28036 m= 1926 mr = 7890 m= 195 mr = 1356 m= 5 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 90 time to turn everything in is 1.620000 number of dielectric boundary points 74781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 18296 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) : 1.941324 object centre at (A) : 13.66900 38.95250 24.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3515623 2.3069645E-03 midg,1,midg; midg,igrid,midg 0.2297007 0.7251158 1,midg,midg; igrid,midg,midg 0.5403933 8.4725820E-02 gauss-seidel spectral radius is 0.9992741 estimated iterations to convergence 293 setup time was (sec) 1.960000 now iterating at: 23:09:45 rms-change max change #iterations 9.767609 370.6611 at 10iterations 5.774541 135.3758 at 20iterations 3.394498 72.53862 at 30iterations 1.982740 41.97478 at 40iterations 1.156921 22.67174 at 50iterations 0.6740013 14.37887 at 60iterations 0.3921319 7.817596 at 70iterations 0.2280958 4.756115 at 80iterations 0.1323262 2.687002 at 90iterations 7.6891474E-02 1.388861 at 100iterations 4.4458393E-02 0.8362026 at 110iterations 2.5826281E-02 0.4826000 at 120iterations 1.4943528E-02 0.2856293 at 130iterations 8.7064775E-03 0.1740923 at 140iterations 5.0565181E-03 9.7381592E-02 at 150iterations 2.9581469E-03 6.4207077E-02 at 160iterations 1.7431384E-03 3.6018372E-02 at 170iterations 1.0474114E-03 2.3241043E-02 at 180iterations finished qdiffx linear iterations at : 23:10:02 total time elapsed so far: 18.92000 # loops : 180 mean,max change (kT/e) : 1.0474114E-03 2.3241043E-02 energy calculations done at 18.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.09000 DelPhi exited at 23:10:03 19.098u 0.464s 0:19.87 98.3% 0+0k 0+0io 0pf+0w