Sat Oct 8 22:41:30 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 22:41:30 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: MG6 609 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5885757 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): 82.00800 125.5820 ymin,ymax (A): 61.01500 121.5000 zmin,zma (A): 54.83800 109.7280 x,y,z range (A): 43.57400 60.48500 54.89000 scale (grids/A): 0.5885757 object centre (A): 103.7950 91.25750 82.28300 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 11.90002 assigned positive charge : 383.0529 centred at (gu) : 90.03770 89.79114 89.35914 assigned negative charge : -371.1538 centred at (gu) : 89.99189 89.76861 89.41294 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6043 nv = 96 ne = 84 npr = 51898 no. pairs analyzed = 51898 no. exposed pairs = 3346 no. arc points = 23447 no. surface atoms = 1131 nbur = 1460 mkacc time = 0.1500000 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 = 1.484000 m= 296 mr = 3148 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2449 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7578 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5340315E-09 1.8849862E-09 midg,1,midg; midg,igrid,midg 3.0709491E-09 3.8438106E-09 1,midg,midg; igrid,midg,midg 2.3417515E-09 4.6299502E-09 gauss-seidel spectral radius is 0.9850706 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 22:41:31 rms-change max change #iterations 9.6431844E-02 15.39930 at 10iterations 8.9031765E-03 1.391609 at 20iterations 1.3928129E-03 0.2703438 at 30iterations 3.9136736E-04 8.2141876E-02 at 40iterations 1.2298915E-04 2.5737762E-02 at 50iterations finished qdiffx linear iterations at : 22:41:34 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.2298915E-04 2.5737762E-02 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 22:41:35 4.066u 0.263s 0:04.60 93.9% 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 22:41:35 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: MG6 609 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.765727 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): 82.00800 125.5820 ymin,ymax (A): 61.01500 121.5000 zmin,zma (A): 54.83800 109.7280 x,y,z range (A): 43.57400 60.48500 54.89000 scale (grids/A): 1.765727 object centre (A): 103.7950 91.25750 82.28300 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 11.90002 assigned positive charge : 383.0529 centred at (gu) : 90.11224 89.37294 88.07720 assigned negative charge : -371.1538 centred at (gu) : 89.97554 89.30560 88.23885 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 65633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23447 grid for indexing accessible points = 1.400000 m= 22422 mr = 44272 m= 2883 mr = 15875 m= 121 mr = 1604 m= 0 mr = 24 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 29284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 210 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19080 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) : 0.5885757 object centre at (A) : 103.7950 91.25750 82.28300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9542256E-02 7.6134838E-03 midg,1,midg; midg,igrid,midg 2.9065774E-04 3.8149420E-02 1,midg,midg; igrid,midg,midg 7.4145496E-03 1.7633522E-02 gauss-seidel spectral radius is 0.9984236 estimated iterations to convergence 200 setup time was (sec) 0.8900000 now iterating at: 22:41:36 rms-change max change #iterations 3.578090 186.4608 at 10iterations 1.574391 56.25431 at 20iterations 0.6934282 25.46786 at 30iterations 0.3076535 12.88908 at 40iterations 0.1366544 5.007308 at 50iterations 6.0459342E-02 1.919647 at 60iterations 2.7004626E-02 0.9466887 at 70iterations 1.2180164E-02 0.4283218 at 80iterations 5.6177960E-03 0.2108383 at 90iterations 2.7359764E-03 0.1133652 at 100iterations 1.4212162E-03 6.0203552E-02 at 110iterations 8.1536022E-04 3.4496307E-02 at 120iterations finished qdiffx linear iterations at : 22:41:44 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 8.1536022E-04 3.4496307E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 22:41:45 9.305u 0.299s 0:09.89 96.9% 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 22:41:45 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: MG6 609 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.648591 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): 82.00800 125.5820 ymin,ymax (A): 61.01500 121.5000 zmin,zma (A): 54.83800 109.7280 x,y,z range (A): 43.57400 60.48500 54.89000 scale (grids/A): 2.648591 object centre (A): 103.7950 91.25750 82.28300 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 11.90002 assigned positive charge : 383.0529 centred at (gu) : 90.16817 89.05917 87.11562 assigned negative charge : -371.1538 centred at (gu) : 89.96335 88.95838 87.35829 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 151848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23447 grid for indexing accessible points = 1.400000 m= 74218 mr = 107977 m= 24610 mr = 59271 m= 4884 mr = 19044 m= 546 mr = 3478 m= 11 mr = 325 m= 0 mr = 7 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 66015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 19628 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) : 1.765727 object centre at (A) : 103.7950 91.25750 82.28300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3657841 2.3120979E-02 midg,1,midg; midg,igrid,midg -1.2209997E-02 0.6440144 1,midg,midg; igrid,midg,midg 7.8048624E-02 0.2199105 gauss-seidel spectral radius is 0.9992064 estimated iterations to convergence 280 setup time was (sec) 1.800000 now iterating at: 22:41:47 rms-change max change #iterations 8.896542 319.6307 at 10iterations 5.147860 136.1107 at 20iterations 2.966841 68.01254 at 30iterations 1.694161 39.00789 at 40iterations 0.9652674 26.09407 at 50iterations 0.5490802 12.87268 at 60iterations 0.3119098 7.076004 at 70iterations 0.1769438 4.011795 at 80iterations 0.1003281 2.024076 at 90iterations 5.6531064E-02 1.200966 at 100iterations 3.2085106E-02 0.6737480 at 110iterations 1.8281598E-02 0.3781796 at 120iterations 1.0413265E-02 0.2185993 at 130iterations 6.0051009E-03 0.1380596 at 140iterations 3.5283552E-03 8.1890106E-02 at 150iterations 2.1463062E-03 5.7657242E-02 at 160iterations 1.3626661E-03 3.3226013E-02 at 170iterations 9.2153088E-04 2.4070740E-02 at 180iterations finished qdiffx linear iterations at : 22:42:00 total time elapsed so far: 15.29000 # loops : 180 mean,max change (kT/e) : 9.2153088E-04 2.4070740E-02 energy calculations done at 15.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.47000 DelPhi exited at 22:42:01 15.469u 0.304s 0:16.04 98.2% 0+0k 0+0io 0pf+0w