Sat Oct 15 12:13:01 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 Sat Oct 15 2011 at 12:13:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3507 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: 0.5391163 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): -46.60700 7.404000 ymin,ymax (A): 172.6540 236.4780 zmin,zma (A): 78.27400 144.3080 x,y,z range (A): 54.01100 63.82402 66.03400 scale (grids/A): 0.5391163 object centre (A): -19.60150 204.5660 111.2910 number of atom coordinates read : 3507 total number of charged atoms : 3362 net assigned charge : 11.50003 assigned positive charge : 518.7571 centred at (gu) : 89.54479 90.06456 90.19463 assigned negative charge : -507.2591 centred at (gu) : 89.44341 89.99841 90.31487 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6727 nv = 96 ne = 84 npr = 68120 no. pairs analyzed = 68120 no. exposed pairs = 4768 no. arc points = 33662 no. surface atoms = 1581 nbur = 1926 mkacc time = 0.1100000 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 = 1.568000 m= 280 mr = 3309 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2500000 number of dielectric boundary points 3687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3296 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8863 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1847288E-09 -1.7292125E-10 midg,1,midg; midg,igrid,midg 1.5852494E-10 9.4973629E-10 1,midg,midg; igrid,midg,midg -5.9367761E-11 1.0149531E-09 gauss-seidel spectral radius is 0.9823182 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 12:13:02 rms-change max change #iterations 7.4327268E-02 13.41612 at 10iterations 4.7216867E-03 0.8168564 at 20iterations 3.1325777E-04 4.5120239E-02 at 30iterations 2.2814298E-05 3.5171509E-03 at 40iterations 2.3521252E-06 2.8419495E-04 at 50iterations finished qdiffx linear iterations at : 12:13:05 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.3521252E-06 2.8419495E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 12:13:06 3.473u 0.174s 0:04.47 81.4% 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 15 2011 at 12:13:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3507 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: 1.617349 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): -46.60700 7.404000 ymin,ymax (A): 172.6540 236.4780 zmin,zma (A): 78.27400 144.3080 x,y,z range (A): 54.01100 63.82402 66.03400 scale (grids/A): 1.617349 object centre (A): -19.60150 204.5660 111.2910 number of atom coordinates read : 3507 total number of charged atoms : 3362 net assigned charge : 11.50003 assigned positive charge : 518.7571 centred at (gu) : 88.63340 90.19219 90.58294 assigned negative charge : -507.2591 centred at (gu) : 88.32997 89.99497 90.94414 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33662 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22795 mr = 49663 m= 2311 mr = 15133 m= 74 mr = 1107 m= 0 mr = 1 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1096 time to turn everything in is 0.3700000 number of dielectric boundary points 34423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 25763 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) : 0.5391163 object centre at (A) : -19.60150 204.5660 111.2910 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6254127E-03 -1.0387667E-02 midg,1,midg; midg,igrid,midg 6.4862855E-03 2.2222033E-02 1,midg,midg; igrid,midg,midg -8.0771570E-04 1.2132097E-02 gauss-seidel spectral radius is 0.9982206 estimated iterations to convergence 188 setup time was (sec) 0.6000000 now iterating at: 12:13:07 rms-change max change #iterations 3.529128 181.1933 at 10iterations 1.476736 58.29844 at 20iterations 0.6203043 22.27418 at 30iterations 0.2600411 9.514132 at 40iterations 0.1085679 3.620572 at 50iterations 4.5688789E-02 1.670094 at 60iterations 1.9222740E-02 0.6705647 at 70iterations 8.0883019E-03 0.2701492 at 80iterations 3.3910901E-03 0.1188507 at 90iterations 1.4286722E-03 5.0949097E-02 at 100iterations 6.0330576E-04 2.1095276E-02 at 110iterations 2.5422071E-04 8.3370209E-03 at 120iterations finished qdiffx linear iterations at : 12:13:14 total time elapsed so far: 8.360000 # loops : 120 mean,max change (kT/e) : 2.5422071E-04 8.3370209E-03 energy calculations done at 8.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.500000 DelPhi exited at 12:13:15 8.501u 0.217s 0:09.11 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 Sat Oct 15 2011 at 12:13:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3507 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: 2.426023 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): -46.60700 7.404000 ymin,ymax (A): 172.6540 236.4780 zmin,zma (A): 78.27400 144.3080 x,y,z range (A): 54.01100 63.82402 66.03400 scale (grids/A): 2.426023 object centre (A): -19.60150 204.5660 111.2910 number of atom coordinates read : 3507 total number of charged atoms : 3362 net assigned charge : 11.50003 assigned positive charge : 518.7571 centred at (gu) : 87.94978 90.28811 90.87416 assigned negative charge : -507.2591 centred at (gu) : 87.49495 89.99224 91.41637 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 174683 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33662 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 78760 mr = 122424 m= 22061 mr = 60760 m= 3571 mr = 16103 m= 247 mr = 2276 m= 2 mr = 85 m= 1 mr = 0 m= 1 mr = 0 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 3985 time to turn everything in is 0.9700000 number of dielectric boundary points 77679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 26862 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) : 1.617349 object centre at (A) : -19.60150 204.5660 111.2910 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2388151 -0.1215269 midg,1,midg; midg,igrid,midg 2.5669560E-02 0.4087930 1,midg,midg; igrid,midg,midg -7.6556951E-02 0.1427106 gauss-seidel spectral radius is 0.9991708 estimated iterations to convergence 274 setup time was (sec) 1.250000 now iterating at: 12:13:16 rms-change max change #iterations 9.203795 317.7186 at 10iterations 5.266879 115.2362 at 20iterations 2.998001 78.38184 at 30iterations 1.698065 43.98457 at 40iterations 0.9569277 19.49581 at 50iterations 0.5372782 11.18014 at 60iterations 0.3001993 6.577374 at 70iterations 0.1676777 3.468739 at 80iterations 9.3902938E-02 1.867509 at 90iterations 5.2449126E-02 0.9587355 at 100iterations 2.9116770E-02 0.6107149 at 110iterations 1.6269637E-02 0.3154945 at 120iterations 9.0733562E-03 0.1793041 at 130iterations 5.0407960E-03 9.6690178E-02 at 140iterations 2.8031534E-03 5.4910660E-02 at 150iterations 1.5575298E-03 2.9210091E-02 at 160iterations 8.6596532E-04 1.6612053E-02 at 170iterations 4.8192602E-04 9.1571808E-03 at 180iterations finished qdiffx linear iterations at : 12:13:29 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 4.8192602E-04 9.1571808E-03 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 12:13:29 13.280u 0.280s 0:14.26 95.0% 0+0k 0+0io 0pf+0w