Sat Oct 8 19:33:19 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 8 2011 at 19:33:19 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 344 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: 0.6291753 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): -31.88800 17.47600 ymin,ymax (A): -23.38000 24.31100 zmin,zma (A): -12.20600 44.37600 x,y,z range (A): 49.36400 47.69100 56.58200 scale (grids/A): 0.6291753 object centre (A): -7.206000 0.4654999 16.08500 number of atom coordinates read : 2567 total number of charged atoms : 2437 net assigned charge : 3.220010 assigned positive charge : 391.2871 centred at (gu) : 88.50169 88.74751 89.88121 assigned negative charge : -388.0676 centred at (gu) : 88.44999 88.80901 89.73679 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6707 nv = 96 ne = 84 npr = 53070 no. pairs analyzed = 53070 no. exposed pairs = 3020 no. arc points = 21506 no. surface atoms = 1022 nbur = 1545 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 323 mr = 3725 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.2800000 number of dielectric boundary points 3273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2179 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4479518E-09 1.5264522E-08 midg,1,midg; midg,igrid,midg 1.1427550E-08 -1.4001004E-09 1,midg,midg; igrid,midg,midg -1.5416375E-09 5.6975757E-09 gauss-seidel spectral radius is 0.9869103 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 19:33:20 rms-change max change #iterations 0.1386319 21.99014 at 10iterations 1.3512400E-02 2.170853 at 20iterations 1.2803903E-03 0.1784477 at 30iterations 1.2471521E-04 1.7776489E-02 at 40iterations 1.2500559E-05 1.7471313E-03 at 50iterations finished qdiffx linear iterations at : 19:33:23 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.2500559E-05 1.7471313E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 19:33:23 3.584u 0.215s 0:04.07 93.1% 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 8 2011 at 19:33:23 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 344 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: 1.887526 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): -31.88800 17.47600 ymin,ymax (A): -23.38000 24.31100 zmin,zma (A): -12.20600 44.37600 x,y,z range (A): 49.36400 47.69100 56.58200 scale (grids/A): 1.887526 object centre (A): -7.206000 0.4654999 16.08500 number of atom coordinates read : 2567 total number of charged atoms : 2437 net assigned charge : 3.220010 assigned positive charge : 391.2871 centred at (gu) : 85.50450 86.24190 89.64304 assigned negative charge : -388.0676 centred at (gu) : 85.34978 86.42671 89.21011 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21506 grid for indexing accessible points = 1.400000 m= 26243 mr = 50535 m= 3846 mr = 19583 m= 167 mr = 2278 m= 5 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2858 time to turn everything in is 0.5200000 number of dielectric boundary points 30150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19179 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) : 0.6291753 object centre at (A) : -7.206000 0.4654999 16.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2563817E-02 2.5157958E-02 midg,1,midg; midg,igrid,midg 1.7777367E-02 1.6019561E-03 1,midg,midg; igrid,midg,midg -9.5444627E-04 2.7917985E-02 gauss-seidel spectral radius is 0.9986055 estimated iterations to convergence 212 setup time was (sec) 0.8300000 now iterating at: 19:33:24 rms-change max change #iterations 4.166523 177.4121 at 10iterations 1.938303 66.17084 at 20iterations 0.8991019 34.06052 at 30iterations 0.4165694 13.45501 at 40iterations 0.1936203 7.010998 at 50iterations 9.0322129E-02 2.831009 at 60iterations 4.1931406E-02 1.260635 at 70iterations 1.9550357E-02 0.6221466 at 80iterations 9.0669990E-03 0.3040204 at 90iterations 4.2097201E-03 0.1343002 at 100iterations 1.9576396E-03 6.0071945E-02 at 110iterations 9.0967503E-04 2.8259277E-02 at 120iterations finished qdiffx linear iterations at : 19:33:31 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 9.0967503E-04 2.8259277E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 19:33:32 7.802u 0.254s 0:08.35 96.4% 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 8 2011 at 19:33:32 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN3 344 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: 2.831289 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): -31.88800 17.47600 ymin,ymax (A): -23.38000 24.31100 zmin,zma (A): -12.20600 44.37600 x,y,z range (A): 49.36400 47.69100 56.58200 scale (grids/A): 2.831289 object centre (A): -7.206000 0.4654999 16.08500 number of atom coordinates read : 2567 total number of charged atoms : 2437 net assigned charge : 3.220010 assigned positive charge : 391.2871 centred at (gu) : 83.25659 84.36288 89.46452 assigned negative charge : -388.0676 centred at (gu) : 83.02464 84.63998 88.81508 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 167287 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21506 grid for indexing accessible points = 1.400000 m= 85235 mr = 122200 m= 30512 mr = 70489 m= 6591 mr = 24539 m= 791 mr = 4885 m= 44 mr = 485 m= 0 mr = 13 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 9833 time to turn everything in is 1.340000 number of dielectric boundary points 67849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 19494 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) : 1.887526 object centre at (A) : -7.206000 0.4654999 16.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0536720E-02 0.2702303 midg,1,midg; midg,igrid,midg 0.1926754 3.5463650E-02 1,midg,midg; igrid,midg,midg 2.1280868E-02 0.3321411 gauss-seidel spectral radius is 0.9992452 estimated iterations to convergence 287 setup time was (sec) 1.680000 now iterating at: 19:33:33 rms-change max change #iterations 9.720645 352.6499 at 10iterations 5.603289 211.3474 at 20iterations 3.204901 67.47975 at 30iterations 1.834269 34.61638 at 40iterations 1.049363 21.28032 at 50iterations 0.6000464 11.82132 at 60iterations 0.3433804 6.260835 at 70iterations 0.1958694 3.874710 at 80iterations 0.1118165 2.327826 at 90iterations 6.3824184E-02 1.226288 at 100iterations 3.6542401E-02 0.6723976 at 110iterations 2.0836223E-02 0.4186993 at 120iterations 1.1893357E-02 0.2405224 at 130iterations 6.7991349E-03 0.1280193 at 140iterations 3.8816025E-03 7.6637268E-02 at 150iterations 2.2144374E-03 4.6768188E-02 at 160iterations 1.2665744E-03 2.5924683E-02 at 170iterations 7.2585588E-04 1.3639450E-02 at 180iterations finished qdiffx linear iterations at : 19:33:46 total time elapsed so far: 14.48000 # loops : 180 mean,max change (kT/e) : 7.2585588E-04 1.3639450E-02 energy calculations done at 14.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.66000 DelPhi exited at 19:33:47 14.658u 0.258s 0:15.25 97.7% 0+0k 0+0io 0pf+0w