Tue Oct 11 05:27:46 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 05:27:46 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 = 2053 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: 0.6994793 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): 25.62200 72.86100 ymin,ymax (A): -20.99200 29.90300 zmin,zma (A): 3.844000 46.52400 x,y,z range (A): 47.23900 50.89500 42.68000 scale (grids/A): 0.6994793 object centre (A): 49.24150 4.455501 25.18400 number of atom coordinates read : 2053 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 88.74669 91.18501 90.11340 assigned negative charge : -305.0792 centred at (gu) : 88.86076 91.10983 90.18777 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6862 nv = 96 ne = 84 npr = 41006 no. pairs analyzed = 41006 no. exposed pairs = 2524 no. arc points = 17186 no. surface atoms = 857 nbur = 1196 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 406 mr = 3885 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1628 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7645 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2394052E-08 1.4311065E-08 midg,1,midg; midg,igrid,midg 1.1324340E-08 9.3750884E-08 1,midg,midg; igrid,midg,midg 1.1486791E-07 -1.2329194E-09 gauss-seidel spectral radius is 0.9893462 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 05:27:47 rms-change max change #iterations 0.1870112 28.69952 at 10iterations 2.2842865E-02 3.440567 at 20iterations 2.9613210E-03 0.3967171 at 30iterations 4.9566239E-04 7.4813843E-02 at 40iterations 1.2469637E-04 1.4545441E-02 at 50iterations finished qdiffx linear iterations at : 05:27:51 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 1.2469637E-04 1.4545441E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 05:27:52 4.385u 0.381s 0:05.47 87.0% 0+0k 0+0io 6pf+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 05:27:52 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 = 2053 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: 2.098438 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): 25.62200 72.86100 ymin,ymax (A): -20.99200 29.90300 zmin,zma (A): 3.844000 46.52400 x,y,z range (A): 47.23900 50.89500 42.68000 scale (grids/A): 2.098438 object centre (A): 49.24150 4.455501 25.18400 number of atom coordinates read : 2053 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 86.23999 93.55524 90.34024 assigned negative charge : -305.0792 centred at (gu) : 86.58250 93.32961 90.56351 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17186 grid for indexing accessible points = 1.400000 m= 29219 mr = 51174 m= 5600 mr = 22342 m= 444 mr = 3687 m= 9 mr = 217 m= 0 mr = 3 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 30233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15270 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) : 0.6994793 object centre at (A) : 49.24150 4.455501 25.18400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5397139E-02 2.4463037E-02 midg,1,midg; midg,igrid,midg 3.4769982E-02 4.4099357E-02 1,midg,midg; igrid,midg,midg 4.2367905E-02 -3.3225432E-02 gauss-seidel spectral radius is 0.9988054 estimated iterations to convergence 229 setup time was (sec) 0.9400000 now iterating at: 05:27:53 rms-change max change #iterations 4.452537 203.5889 at 10iterations 2.180837 70.34340 at 20iterations 1.074800 34.30064 at 30iterations 0.5300854 16.75652 at 40iterations 0.2615471 7.783097 at 50iterations 0.1286131 4.023381 at 60iterations 6.3079394E-02 1.857349 at 70iterations 3.1316198E-02 0.9758148 at 80iterations 1.5551635E-02 0.5036812 at 90iterations 7.7509047E-03 0.2359428 at 100iterations 3.8956902E-03 0.1182752 at 110iterations 2.0077250E-03 6.1565399E-02 at 120iterations finished qdiffx linear iterations at : 05:28:02 total time elapsed so far: 10.30000 # loops : 120 mean,max change (kT/e) : 2.0077250E-03 6.1565399E-02 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.47000 DelPhi exited at 05:28:03 10.471u 0.429s 0:11.28 96.5% 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 05:28:03 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 = 2053 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: 3.147657 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): 25.62200 72.86100 ymin,ymax (A): -20.99200 29.90300 zmin,zma (A): 3.844000 46.52400 x,y,z range (A): 47.23900 50.89500 42.68000 scale (grids/A): 3.147657 object centre (A): 49.24150 4.455501 25.18400 number of atom coordinates read : 2053 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.5790 centred at (gu) : 84.35991 95.33286 90.51039 assigned negative charge : -305.0792 centred at (gu) : 84.87374 94.99447 90.84528 start vw surface at 0.1100000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 166613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17186 grid for indexing accessible points = 1.400000 m= 90934 mr = 123233 m= 37200 mr = 75703 m= 10455 mr = 30611 m= 2002 mr = 8207 m= 193 mr = 1426 m= 10 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.970000 number of dielectric boundary points 68108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 15400 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) : 2.098438 object centre at (A) : 49.24150 4.455501 25.18400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1660657 0.2082610 midg,1,midg; midg,igrid,midg 0.2645433 0.3559603 1,midg,midg; igrid,midg,midg 0.3810711 -0.3497665 gauss-seidel spectral radius is 0.9992896 estimated iterations to convergence 296 setup time was (sec) 2.290000 now iterating at: 05:28:06 rms-change max change #iterations 9.966423 491.9397 at 10iterations 5.874139 139.5751 at 20iterations 3.460992 78.46132 at 30iterations 2.034651 39.82051 at 40iterations 1.192315 24.71568 at 50iterations 0.6997821 13.70080 at 60iterations 0.4102318 7.950385 at 70iterations 0.2402889 4.130394 at 80iterations 0.1402315 2.656029 at 90iterations 8.2016207E-02 1.489273 at 100iterations 4.8075330E-02 0.8889527 at 110iterations 2.8253496E-02 0.5707741 at 120iterations 1.6735554E-02 0.2996969 at 130iterations 1.0043248E-02 0.1920090 at 140iterations 6.1814468E-03 0.1158829 at 150iterations 3.9540818E-03 7.5485229E-02 at 160iterations 2.6773149E-03 4.9713135E-02 at 170iterations 1.9228418E-03 3.6586761E-02 at 180iterations finished qdiffx linear iterations at : 05:28:22 total time elapsed so far: 18.11000 # loops : 180 mean,max change (kT/e) : 1.9228418E-03 3.6586761E-02 energy calculations done at 18.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.28000 DelPhi exited at 05:28:22 18.284u 0.453s 0:19.09 98.1% 0+0k 0+0io 0pf+0w