Sat Oct 15 11:28:13 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 15 2011 at 11:28:13 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: HIZ 12 has a net charge of 0.2000 !!! WARNING: HIZ 14 has a net charge of 0.2000 !!! WARNING: HIZ 211 has a net charge of 0.2000 !!! WARNING: GLM 214 has a net charge of -0.0940 !!! WARNING: ZN6 699 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6331140 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): -53.24600 2.984000 ymin,ymax (A): -35.93000 17.63100 zmin,zma (A): -20.71600 30.90000 x,y,z range (A): 56.23000 53.56100 51.61600 scale (grids/A): 0.6331140 object centre (A): -25.13100 -9.149500 5.092000 number of atom coordinates read : 3322 total number of charged atoms : 3193 net assigned charge : -4.093974 assigned positive charge : 508.3325 centred at (gu) : 91.33286 90.64237 90.17124 assigned negative charge : -512.4276 centred at (gu) : 91.39906 90.45517 90.29739 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8811 nv = 96 ne = 84 npr = 69395 no. pairs analyzed = 69395 no. exposed pairs = 3612 no. arc points = 24825 no. surface atoms = 1253 nbur = 2069 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 5412 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.3900000 number of dielectric boundary points 3782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2400 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0557059E-08 -2.1915643E-08 midg,1,midg; midg,igrid,midg -2.5343510E-08 2.1333619E-08 1,midg,midg; igrid,midg,midg 2.5660951E-09 -1.7819550E-08 gauss-seidel spectral radius is 0.9871283 estimated iterations to convergence 72 setup time was (sec) 0.6900000 now iterating at: 11:28:14 rms-change max change #iterations 0.1657867 25.39800 at 10iterations 1.6285116E-02 1.905956 at 20iterations 1.6067645E-03 0.2276077 at 30iterations 1.5910019E-04 2.0019531E-02 at 40iterations 1.5895310E-05 1.9969940E-03 at 50iterations finished qdiffx linear iterations at : 11:28:19 total time elapsed so far: 5.130000 # loops : 50 mean,max change (kT/e) : 1.5895310E-05 1.9969940E-03 energy calculations done at 5.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.290000 DelPhi exited at 11:28:19 5.295u 0.460s 0:06.11 94.1% 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 Sat Oct 15 2011 at 11:28:20 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: HIZ 12 has a net charge of 0.2000 !!! WARNING: HIZ 14 has a net charge of 0.2000 !!! WARNING: HIZ 211 has a net charge of 0.2000 !!! WARNING: GLM 214 has a net charge of -0.0940 !!! WARNING: ZN6 699 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: 1.899342 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): -53.24600 2.984000 ymin,ymax (A): -35.93000 17.63100 zmin,zma (A): -20.71600 30.90000 x,y,z range (A): 56.23000 53.56100 51.61600 scale (grids/A): 1.899342 object centre (A): -25.13100 -9.149500 5.092000 number of atom coordinates read : 3322 total number of charged atoms : 3193 net assigned charge : -4.093974 assigned positive charge : 508.3325 centred at (gu) : 93.99745 91.92633 90.51296 assigned negative charge : -512.4276 centred at (gu) : 94.19676 91.36524 90.89140 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 96241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24825 grid for indexing accessible points = 1.400000 m= 35770 mr = 70984 m= 5452 mr = 27959 m= 306 mr = 3660 m= 1 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 3785 time to turn everything in is 0.7700000 number of dielectric boundary points 35071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 25110 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) : 0.6331140 object centre at (A) : -25.13100 -9.149500 5.092000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2092147E-03 -6.7034699E-02 midg,1,midg; midg,igrid,midg -3.7089411E-02 3.5173092E-02 1,midg,midg; igrid,midg,midg 1.5771833E-03 -3.8196687E-02 gauss-seidel spectral radius is 0.9986830 estimated iterations to convergence 218 setup time was (sec) 1.130000 now iterating at: 11:28:21 rms-change max change #iterations 4.971313 188.5366 at 10iterations 2.356897 71.52744 at 20iterations 1.119403 31.72768 at 30iterations 0.5323349 14.69092 at 40iterations 0.2529046 6.988070 at 50iterations 0.1206083 3.233717 at 60iterations 5.7320248E-02 1.735855 at 70iterations 2.7319442E-02 0.7240295 at 80iterations 1.2961553E-02 0.3708200 at 90iterations 6.1789444E-03 0.1685734 at 100iterations 2.9428564E-03 8.0079079E-02 at 110iterations 1.4003228E-03 3.8543701E-02 at 120iterations finished qdiffx linear iterations at : 11:28:33 total time elapsed so far: 12.84000 # loops : 120 mean,max change (kT/e) : 1.4003228E-03 3.8543701E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 11:28:34 13.009u 0.519s 0:14.17 95.3% 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 Sat Oct 15 2011 at 11:28:34 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3322 !!! WARNING: HIZ 12 has a net charge of 0.2000 !!! WARNING: HIZ 14 has a net charge of 0.2000 !!! WARNING: HIZ 211 has a net charge of 0.2000 !!! WARNING: GLM 214 has a net charge of -0.0940 !!! WARNING: ZN6 699 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.849013 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): -53.24600 2.984000 ymin,ymax (A): -35.93000 17.63100 zmin,zma (A): -20.71600 30.90000 x,y,z range (A): 56.23000 53.56100 51.61600 scale (grids/A): 2.849013 object centre (A): -25.13100 -9.149500 5.092000 number of atom coordinates read : 3322 total number of charged atoms : 3193 net assigned charge : -4.093974 assigned positive charge : 508.3325 centred at (gu) : 95.99596 92.88932 90.76939 assigned negative charge : -512.4276 centred at (gu) : 96.29485 92.04773 91.33699 start vw surface at 0.1300000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 222989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24825 grid for indexing accessible points = 1.400000 m= 116778 mr = 170925 m= 42733 mr = 99048 m= 9954 mr = 36028 m= 1337 mr = 7866 m= 51 mr = 904 m= 0 mr = 16 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 13490 time to turn everything in is 2.060000 number of dielectric boundary points 79055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 25542 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) : 1.899342 object centre at (A) : -25.13100 -9.149500 5.092000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2215108 -0.7774046 midg,1,midg; midg,igrid,midg -0.3224120 0.3842182 1,midg,midg; igrid,midg,midg 0.1371937 -0.5262315 gauss-seidel spectral radius is 0.9992751 estimated iterations to convergence 293 setup time was (sec) 2.460000 now iterating at: 11:28:37 rms-change max change #iterations 11.45181 355.7491 at 10iterations 6.704649 127.1287 at 20iterations 3.905758 73.63454 at 30iterations 2.274757 44.78117 at 40iterations 1.319050 21.32321 at 50iterations 0.7656416 12.45425 at 60iterations 0.4445938 8.272966 at 70iterations 0.2577851 4.407840 at 80iterations 0.1489662 2.322858 at 90iterations 8.6307861E-02 1.421579 at 100iterations 4.9964286E-02 0.8726009 at 110iterations 2.8895112E-02 0.4605484 at 120iterations 1.6747419E-02 0.2567387 at 130iterations 9.6718101E-03 0.1710091 at 140iterations 5.5955565E-03 8.9175701E-02 at 150iterations 3.2404021E-03 5.3664207E-02 at 160iterations 1.8696126E-03 2.9581070E-02 at 170iterations 1.0834490E-03 1.6576767E-02 at 180iterations finished qdiffx linear iterations at : 11:28:56 total time elapsed so far: 22.11000 # loops : 180 mean,max change (kT/e) : 1.0834490E-03 1.6576767E-02 energy calculations done at 22.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.26000 DelPhi exited at 11:28:57 22.268u 0.585s 0:23.16 98.6% 0+0k 0+0io 0pf+0w