Sat Oct 8 11:50:09 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 11:50:09 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4434 !!! WARNING: HIT 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5694997 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): -27.45900 35.05200 ymin,ymax (A): 35.38400 95.25000 zmin,zma (A): 30.90800 89.44500 x,y,z range (A): 62.51100 59.86600 58.53700 scale (grids/A): 0.5694997 object centre (A): 3.796501 65.31700 60.17650 number of atom coordinates read : 4434 total number of charged atoms : 4274 net assigned charge : -6.485953 assigned positive charge : 670.2090 centred at (gu) : 90.57981 89.08643 89.10307 assigned negative charge : -676.6983 centred at (gu) : 90.44799 89.15184 89.29328 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9077 nv = 96 ne = 84 npr = 93699 no. pairs analyzed = 93699 no. exposed pairs = 4972 no. arc points = 33499 no. surface atoms = 1693 nbur = 2741 mkacc time = 0.2400000 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 = 1.512000 m= 399 mr = 5277 m= 0 mr = 33 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 136 time to turn everything in is 0.4900000 number of dielectric boundary points 4166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3451 ## 391 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1396557E-09 -4.5358268E-09 midg,1,midg; midg,igrid,midg 6.0688848E-10 -2.0926705E-09 1,midg,midg; igrid,midg,midg -3.6527184E-09 2.3083329E-09 gauss-seidel spectral radius is 0.9841900 estimated iterations to convergence 65 setup time was (sec) 0.8400000 now iterating at: 11:50:11 rms-change max change #iterations 0.1130191 13.81040 at 10iterations 9.0243546E-03 1.102732 at 20iterations 9.9699304E-04 0.1407318 at 30iterations 2.3935565E-04 2.8119087E-02 at 40iterations 7.8681136E-05 1.0110378E-02 at 50iterations finished qdiffx linear iterations at : 11:50:15 total time elapsed so far: 5.240000 # loops : 50 mean,max change (kT/e) : 7.8681136E-05 1.0110378E-02 energy calculations done at 5.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.420000 DelPhi exited at 11:50:16 5.429u 0.453s 0:06.18 94.9% 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 11:50:16 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4434 !!! WARNING: HIT 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.708499 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): -27.45900 35.05200 ymin,ymax (A): 35.38400 95.25000 zmin,zma (A): 30.90800 89.44500 x,y,z range (A): 62.51100 59.86600 58.53700 scale (grids/A): 1.708499 object centre (A): 3.796501 65.31700 60.17650 number of atom coordinates read : 4434 total number of charged atoms : 4274 net assigned charge : -6.485953 assigned positive charge : 670.2090 centred at (gu) : 91.73802 87.25769 87.30766 assigned negative charge : -676.6983 centred at (gu) : 91.34386 87.45491 87.87904 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 102120 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33499 grid for indexing accessible points = 1.400000 m= 33708 mr = 74355 m= 4108 mr = 24685 m= 110 mr = 2356 m= 0 mr = 20 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5818 time to turn everything in is 0.8400000 number of dielectric boundary points 38630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 33062 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) : 0.5694997 object centre at (A) : 3.796501 65.31700 60.17650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3281317E-02 -3.1523112E-02 midg,1,midg; midg,igrid,midg 1.8937396E-02 -1.7907823E-02 1,midg,midg; igrid,midg,midg -3.3996586E-02 3.7321601E-02 gauss-seidel spectral radius is 0.9984676 estimated iterations to convergence 203 setup time was (sec) 1.200000 now iterating at: 11:50:17 rms-change max change #iterations 4.668750 186.5068 at 10iterations 2.092983 63.61624 at 20iterations 0.9382885 29.20971 at 30iterations 0.4206356 11.60448 at 40iterations 0.1890735 5.257986 at 50iterations 8.4843576E-02 2.329860 at 60iterations 3.8132790E-02 1.133588 at 70iterations 1.7200377E-02 0.4945488 at 80iterations 7.7619092E-03 0.2235966 at 90iterations 3.5334066E-03 9.7914696E-02 at 100iterations 1.6514767E-03 5.2669525E-02 at 110iterations 7.9288747E-04 2.3107529E-02 at 120iterations finished qdiffx linear iterations at : 11:50:29 total time elapsed so far: 12.81000 # loops : 120 mean,max change (kT/e) : 7.9288747E-04 2.3107529E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 11:50:29 12.987u 0.542s 0:13.81 97.9% 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 11:50:30 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4434 !!! WARNING: HIT 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.562749 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): -27.45900 35.05200 ymin,ymax (A): 35.38400 95.25000 zmin,zma (A): 30.90800 89.44500 x,y,z range (A): 62.51100 59.86600 58.53700 scale (grids/A): 2.562749 object centre (A): 3.796501 65.31700 60.17650 number of atom coordinates read : 4434 total number of charged atoms : 4274 net assigned charge : -6.485953 assigned positive charge : 670.2090 centred at (gu) : 92.60689 85.88627 85.96107 assigned negative charge : -676.6983 centred at (gu) : 92.01560 86.18226 86.81849 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 237536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33499 grid for indexing accessible points = 1.400000 m= 115972 mr = 180608 m= 35557 mr = 95429 m= 6895 mr = 28020 m= 630 mr = 5067 m= 12 mr = 348 m= 0 mr = 2 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 19024 time to turn everything in is 2.140000 number of dielectric boundary points 87128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 34174 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) : 1.708499 object centre at (A) : 3.796501 65.31700 60.17650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7137972 -0.3667277 midg,1,midg; midg,igrid,midg 0.3185241 -0.2973796 1,midg,midg; igrid,midg,midg -0.3706571 0.4241606 gauss-seidel spectral radius is 0.9992400 estimated iterations to convergence 286 setup time was (sec) 2.540000 now iterating at: 11:50:33 rms-change max change #iterations 11.57879 356.4993 at 10iterations 6.753102 144.3309 at 20iterations 3.916803 71.52486 at 30iterations 2.261384 41.09428 at 40iterations 1.302352 22.02655 at 50iterations 0.7507322 12.56130 at 60iterations 0.4298812 7.019721 at 70iterations 0.2467651 4.409048 at 80iterations 0.1414299 2.443624 at 90iterations 8.0896847E-02 1.349172 at 100iterations 4.6248939E-02 0.7226558 at 110iterations 2.6523840E-02 0.4495082 at 120iterations 1.5188018E-02 0.2495689 at 130iterations 8.7277051E-03 0.1796341 at 140iterations 5.0378591E-03 8.1659317E-02 at 150iterations 2.9290658E-03 5.2120686E-02 at 160iterations 1.7310303E-03 2.7349472E-02 at 170iterations 1.0472523E-03 1.8434525E-02 at 180iterations finished qdiffx linear iterations at : 11:50:52 total time elapsed so far: 22.39000 # loops : 180 mean,max change (kT/e) : 1.0472523E-03 1.8434525E-02 energy calculations done at 22.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.55000 DelPhi exited at 11:50:53 22.554u 0.578s 0:23.44 98.6% 0+0k 0+0io 0pf+0w