Tue Oct 11 04:31:28 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 04:31:28 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 = 2734 !!! WARNING: GLY 174 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6460276 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): -12.12500 36.98800 ymin,ymax (A): -25.80200 22.54400 zmin,zma (A): -9.799001 45.30700 x,y,z range (A): 49.11300 48.34600 55.10600 scale (grids/A): 0.6460276 object centre (A): 12.43150 -1.629001 17.75400 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 3.662014 assigned positive charge : 411.0798 centred at (gu) : 90.29996 90.40536 91.69111 assigned negative charge : -407.4184 centred at (gu) : 90.06335 90.24675 91.63721 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7574 nv = 96 ne = 84 npr = 56468 no. pairs analyzed = 56468 no. exposed pairs = 3283 no. arc points = 22797 no. surface atoms = 1110 nbur = 1624 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 4329 m= 0 mr = 39 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3000000 number of dielectric boundary points 3619 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2318 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9164 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1515955E-09 1.9666746E-08 midg,1,midg; midg,igrid,midg -1.5711002E-08 3.0997782E-08 1,midg,midg; igrid,midg,midg -2.7042395E-08 4.1763379E-08 gauss-seidel spectral radius is 0.9875917 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 04:31:29 rms-change max change #iterations 0.1557257 23.03741 at 10iterations 1.6046483E-02 2.427361 at 20iterations 1.6641491E-03 0.2156472 at 30iterations 1.8945796E-04 2.6393890E-02 at 40iterations 2.7997570E-05 3.6697388E-03 at 50iterations finished qdiffx linear iterations at : 04:31:32 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 2.7997570E-05 3.6697388E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 04:31:32 3.713u 0.415s 0:04.66 88.4% 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 Tue Oct 11 2011 at 04:31:33 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 = 2734 !!! WARNING: GLY 174 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.938083 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): -12.12500 36.98800 ymin,ymax (A): -25.80200 22.54400 zmin,zma (A): -9.799001 45.30700 x,y,z range (A): 49.11300 48.34600 55.10600 scale (grids/A): 1.938083 object centre (A): 12.43150 -1.629001 17.75400 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 3.662014 assigned positive charge : 411.0798 centred at (gu) : 90.89917 91.21542 95.07276 assigned negative charge : -407.4184 centred at (gu) : 90.18948 90.73989 94.91132 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 82020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22797 grid for indexing accessible points = 1.400000 m= 30159 mr = 58247 m= 4582 mr = 22635 m= 252 mr = 2836 m= 4 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1249 time to turn everything in is 0.6300000 number of dielectric boundary points 33215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20348 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) : 0.6460276 object centre at (A) : 12.43150 -1.629001 17.75400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0568864E-02 8.2770921E-03 midg,1,midg; midg,igrid,midg -1.0501709E-02 2.7004717E-02 1,midg,midg; igrid,midg,midg -5.2876011E-03 6.0321644E-02 gauss-seidel spectral radius is 0.9986901 estimated iterations to convergence 219 setup time was (sec) 0.9200000 now iterating at: 04:31:34 rms-change max change #iterations 4.521654 182.2318 at 10iterations 2.154551 71.70782 at 20iterations 1.029553 32.88326 at 30iterations 0.4895931 14.43425 at 40iterations 0.2337333 6.969559 at 50iterations 0.1114636 3.319237 at 60iterations 5.3191680E-02 1.831364 at 70iterations 2.5272518E-02 0.7259817 at 80iterations 1.2085772E-02 0.4145737 at 90iterations 5.7551526E-03 0.1665001 at 100iterations 2.7468870E-03 7.8540802E-02 at 110iterations 1.3082685E-03 3.8208008E-02 at 120iterations finished qdiffx linear iterations at : 04:31:41 total time elapsed so far: 8.550000 # loops : 120 mean,max change (kT/e) : 1.3082685E-03 3.8208008E-02 energy calculations done at 8.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 04:31:42 8.732u 0.435s 0:09.51 96.3% 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 04:31:42 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 = 2734 !!! WARNING: GLY 174 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.907124 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): -12.12500 36.98800 ymin,ymax (A): -25.80200 22.54400 zmin,zma (A): -9.799001 45.30700 x,y,z range (A): 49.11300 48.34600 55.10600 scale (grids/A): 2.907124 object centre (A): 12.43150 -1.629001 17.75400 number of atom coordinates read : 2734 total number of charged atoms : 2582 net assigned charge : 3.662014 assigned positive charge : 411.0798 centred at (gu) : 91.34861 91.82286 97.60904 assigned negative charge : -407.4184 centred at (gu) : 90.28418 91.10979 97.36693 start vw surface at 0.1100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 189422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22797 grid for indexing accessible points = 1.400000 m= 97774 mr = 140419 m= 35297 mr = 80926 m= 8171 mr = 28788 m= 1011 mr = 6039 m= 47 mr = 659 m= 0 mr = 17 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 3954 time to turn everything in is 1.660000 number of dielectric boundary points 74874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 20643 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) : 1.938083 object centre at (A) : 12.43150 -1.629001 17.75400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4731273 0.3077893 midg,1,midg; midg,igrid,midg -0.1289076 0.3151391 1,midg,midg; igrid,midg,midg -4.8048496E-03 0.5101451 gauss-seidel spectral radius is 0.9992697 estimated iterations to convergence 292 setup time was (sec) 1.990000 now iterating at: 04:31:44 rms-change max change #iterations 10.44986 343.7889 at 10iterations 6.125085 148.0281 at 20iterations 3.575314 76.38490 at 30iterations 2.084790 45.45021 at 40iterations 1.212192 23.79541 at 50iterations 0.7033755 13.08677 at 60iterations 0.4086706 7.472614 at 70iterations 0.2362446 4.450226 at 80iterations 0.1369205 2.482052 at 90iterations 7.9040043E-02 1.370569 at 100iterations 4.5697842E-02 0.8195477 at 110iterations 2.6524683E-02 0.4994516 at 120iterations 1.5336002E-02 0.2606010 at 130iterations 8.8698706E-03 0.1737843 at 140iterations 5.1420913E-03 8.7997437E-02 at 150iterations 2.9918728E-03 5.4883957E-02 at 160iterations 1.7480955E-03 3.2695770E-02 at 170iterations 1.0312272E-03 2.2323608E-02 at 180iterations finished qdiffx linear iterations at : 04:31:58 total time elapsed so far: 15.59000 # loops : 180 mean,max change (kT/e) : 1.0312272E-03 2.2323608E-02 energy calculations done at 15.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.77000 DelPhi exited at 04:31:59 15.771u 0.463s 0:16.61 97.7% 0+0k 0+0io 0pf+0w