Tue Oct 11 03:55:00 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 03:55:00 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 !!! WARNING: ARG 32 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6676669 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): -14.85600 32.53900 ymin,ymax (A): 7.556000 55.83600 zmin,zma (A): 25.50100 78.82100 x,y,z range (A): 47.39500 48.28000 53.32000 scale (grids/A): 0.6676669 object centre (A): 8.841501 31.69600 52.16100 number of atom coordinates read : 2751 total number of charged atoms : 2599 net assigned charge : -0.1319869 assigned positive charge : 415.3667 centred at (gu) : 90.45964 90.52863 88.54421 assigned negative charge : -415.4994 centred at (gu) : 90.71197 90.38950 88.63309 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8199 nv = 96 ne = 84 npr = 56927 no. pairs analyzed = 56927 no. exposed pairs = 3333 no. arc points = 23316 no. surface atoms = 1118 nbur = 1633 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 4722 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.2200000 number of dielectric boundary points 3891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9625 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0054281E-08 -1.7394793E-08 midg,1,midg; midg,igrid,midg -3.2911181E-08 3.8745451E-08 1,midg,midg; igrid,midg,midg 5.6798857E-08 -7.3870154E-08 gauss-seidel spectral radius is 0.9883804 estimated iterations to convergence 76 setup time was (sec) 0.4200000 now iterating at: 03:55:00 rms-change max change #iterations 0.1823542 24.30950 at 10iterations 2.0309260E-02 2.537181 at 20iterations 2.2435240E-03 0.2834425 at 30iterations 2.6096561E-04 3.2546997E-02 at 40iterations 3.8321559E-05 4.8637390E-03 at 50iterations finished qdiffx linear iterations at : 03:55:03 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.8321559E-05 4.8637390E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:55:04 3.473u 0.163s 0:04.07 89.1% 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 03:55:04 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 !!! WARNING: ARG 32 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.003001 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): -14.85600 32.53900 ymin,ymax (A): 7.556000 55.83600 zmin,zma (A): 25.50100 78.82100 x,y,z range (A): 47.39500 48.28000 53.32000 scale (grids/A): 2.003001 object centre (A): 8.841501 31.69600 52.16100 number of atom coordinates read : 2751 total number of charged atoms : 2599 net assigned charge : -0.1319869 assigned positive charge : 415.3667 centred at (gu) : 91.37870 91.58504 85.63213 assigned negative charge : -415.4994 centred at (gu) : 92.13573 91.16810 85.89893 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 88055 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23316 grid for indexing accessible points = 1.400000 m= 33376 mr = 62676 m= 5708 mr = 25189 m= 373 mr = 3763 m= 5 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1958 time to turn everything in is 0.4400000 number of dielectric boundary points 35735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 20559 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) : 0.6676669 object centre at (A) : 8.841501 31.69600 52.16100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1160556E-03 -6.2583230E-02 midg,1,midg; midg,igrid,midg -1.8986408E-02 3.3788010E-02 1,midg,midg; igrid,midg,midg 7.2246157E-02 -2.2567732E-02 gauss-seidel spectral radius is 0.9987722 estimated iterations to convergence 226 setup time was (sec) 0.6700000 now iterating at: 03:55:05 rms-change max change #iterations 4.854269 202.2686 at 10iterations 2.375796 87.65442 at 20iterations 1.154938 39.67269 at 30iterations 0.5647797 16.59104 at 40iterations 0.2750670 8.439579 at 50iterations 0.1343692 4.268628 at 60iterations 6.5577500E-02 1.896703 at 70iterations 3.1993888E-02 0.9105277 at 80iterations 1.5606932E-02 0.5061626 at 90iterations 7.5985352E-03 0.2195206 at 100iterations 3.7107065E-03 0.1068897 at 110iterations 1.8175315E-03 4.9343109E-02 at 120iterations finished qdiffx linear iterations at : 03:55:12 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.8175315E-03 4.9343109E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 03:55:12 8.029u 0.185s 0:08.57 95.6% 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 Tue Oct 11 2011 at 03:55:13 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 !!! WARNING: ARG 32 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 3.004501 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): -14.85600 32.53900 ymin,ymax (A): 7.556000 55.83600 zmin,zma (A): 25.50100 78.82100 x,y,z range (A): 47.39500 48.28000 53.32000 scale (grids/A): 3.004501 object centre (A): 8.841501 31.69600 52.16100 number of atom coordinates read : 2751 total number of charged atoms : 2599 net assigned charge : -0.1319869 assigned positive charge : 415.3667 centred at (gu) : 92.06786 92.37754 83.44798 assigned negative charge : -415.4994 centred at (gu) : 93.20355 91.75205 83.84836 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 203387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23316 grid for indexing accessible points = 1.400000 m= 106831 mr = 151006 m= 40559 mr = 88812 m= 10399 mr = 33263 m= 1667 mr = 8091 m= 115 mr = 1192 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 6208 time to turn everything in is 1.140000 number of dielectric boundary points 80544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 20788 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) : 2.003001 object centre at (A) : 8.841501 31.69600 52.16100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2381622 -0.6188077 midg,1,midg; midg,igrid,midg -0.1899549 0.4232804 1,midg,midg; igrid,midg,midg 0.6175588 -0.1478703 gauss-seidel spectral radius is 0.9992915 estimated iterations to convergence 296 setup time was (sec) 1.370000 now iterating at: 03:55:14 rms-change max change #iterations 11.10363 449.5969 at 10iterations 6.545361 128.0458 at 20iterations 3.845436 83.16611 at 30iterations 2.259778 42.97491 at 40iterations 1.322046 27.86391 at 50iterations 0.7745233 13.27838 at 60iterations 0.4520762 7.996582 at 70iterations 0.2643588 4.551088 at 80iterations 0.1543212 2.805147 at 90iterations 8.9936487E-02 1.568823 at 100iterations 5.2528251E-02 0.8955688 at 110iterations 3.0614227E-02 0.5914650 at 120iterations 1.7866060E-02 0.2947226 at 130iterations 1.0416066E-02 0.1678662 at 140iterations 6.0865320E-03 0.1000957 at 150iterations 3.5643338E-03 5.8830261E-02 at 160iterations 2.0919645E-03 3.5446167E-02 at 170iterations 1.2324342E-03 1.9702911E-02 at 180iterations finished qdiffx linear iterations at : 03:55:26 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 1.2324342E-03 1.9702911E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 03:55:26 13.073u 0.229s 0:13.66 97.2% 0+0k 0+0io 0pf+0w