Mon Oct 10 17:03:57 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 Mon Oct 10 2011 at 17:03:57 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4055 !!! WARNING: GLM 98 has a net charge of -0.0940 !!! WARNING: HIR 201 has a net charge of 0.5140 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: 0.5492895 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): -21.57800 40.68200 ymin,ymax (A): -28.22500 22.53300 zmin,zma (A): 11.66500 76.47600 x,y,z range (A): 62.26000 50.75800 64.81100 scale (grids/A): 0.5492895 object centre (A): 9.551999 -2.846001 44.07050 number of atom coordinates read : 4055 total number of charged atoms : 3907 net assigned charge : 7.420032 assigned positive charge : 628.8604 centred at (gu) : 90.82356 90.18336 89.07581 assigned negative charge : -621.4446 centred at (gu) : 90.70602 90.09009 88.93476 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7989 nv = 96 ne = 84 npr = 78128 no. pairs analyzed = 78128 no. exposed pairs = 5904 no. arc points = 40757 no. surface atoms = 1953 nbur = 2102 mkacc time = 0.1400000 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 = 1.540000 m= 374 mr = 3662 m= 0 mr = 17 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 4684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4080 ## 497 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 10440 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2413163E-09 1.5800495E-09 midg,1,midg; midg,igrid,midg -4.3945597E-10 1.5655980E-09 1,midg,midg; igrid,midg,midg -5.8435290E-10 2.1398121E-09 gauss-seidel spectral radius is 0.9830061 estimated iterations to convergence 63 setup time was (sec) 0.4700000 now iterating at: 17:03:57 rms-change max change #iterations 9.0215005E-02 15.85934 at 10iterations 6.2262178E-03 0.9931259 at 20iterations 4.9127702E-04 7.8475952E-02 at 30iterations 7.1444578E-05 8.9416504E-03 at 40iterations 1.6984173E-05 1.5470982E-03 at 50iterations finished qdiffx linear iterations at : 17:04:00 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.6984173E-05 1.5470982E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 17:04:01 3.605u 0.193s 0:04.49 84.4% 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 Mon Oct 10 2011 at 17:04:01 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4055 !!! WARNING: GLM 98 has a net charge of -0.0940 !!! WARNING: HIR 201 has a net charge of 0.5140 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: 1.647869 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): -21.57800 40.68200 ymin,ymax (A): -28.22500 22.53300 zmin,zma (A): 11.66500 76.47600 x,y,z range (A): 62.26000 50.75800 64.81100 scale (grids/A): 1.647869 object centre (A): 9.551999 -2.846001 44.07050 number of atom coordinates read : 4055 total number of charged atoms : 3907 net assigned charge : 7.420032 assigned positive charge : 628.8604 centred at (gu) : 92.46938 90.54847 87.22588 assigned negative charge : -621.4446 centred at (gu) : 92.11776 90.26988 86.80375 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40757 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 28005 mr = 55051 m= 3370 mr = 18020 m= 110 mr = 1396 m= 4 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 43583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 420 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 29982 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) : 0.5492895 object centre at (A) : 9.551999 -2.846001 44.07050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6872839E-03 4.2060588E-02 midg,1,midg; midg,igrid,midg -1.4968959E-03 9.2416545E-03 1,midg,midg; igrid,midg,midg -1.5804445E-02 -1.6207198E-02 gauss-seidel spectral radius is 0.9983522 estimated iterations to convergence 196 setup time was (sec) 0.6500000 now iterating at: 17:04:02 rms-change max change #iterations 4.091320 163.4592 at 10iterations 1.760738 60.50272 at 20iterations 0.7599365 25.56385 at 30iterations 0.3309569 10.79645 at 40iterations 0.1430036 4.889847 at 50iterations 6.2244482E-02 2.172516 at 60iterations 2.6839582E-02 0.8408966 at 70iterations 1.1647426E-02 0.3802299 at 80iterations 5.0851749E-03 0.1840496 at 90iterations 2.2103849E-03 7.1509361E-02 at 100iterations 9.6107152E-04 3.1718731E-02 at 110iterations 4.2025081E-04 1.6145706E-02 at 120iterations finished qdiffx linear iterations at : 17:04:09 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 4.2025081E-04 1.6145706E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 17:04:11 8.021u 0.218s 0:09.56 86.0% 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 Mon Oct 10 2011 at 17:04:11 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4055 !!! WARNING: GLM 98 has a net charge of -0.0940 !!! WARNING: HIR 201 has a net charge of 0.5140 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: 2.471803 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): -21.57800 40.68200 ymin,ymax (A): -28.22500 22.53300 zmin,zma (A): 11.66500 76.47600 x,y,z range (A): 62.26000 50.75800 64.81100 scale (grids/A): 2.471803 object centre (A): 9.551999 -2.846001 44.07050 number of atom coordinates read : 4055 total number of charged atoms : 3907 net assigned charge : 7.420032 assigned positive charge : 628.8604 centred at (gu) : 93.70358 90.82232 85.83845 assigned negative charge : -621.4446 centred at (gu) : 93.17652 90.40472 85.20545 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 200485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40757 grid for indexing accessible points = 1.400000 m= 93566 mr = 136224 m= 29245 mr = 70327 m= 5233 mr = 20722 m= 457 mr = 3022 m= 16 mr = 175 m= 1 mr = 3 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 98531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 31221 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) : 1.647869 object centre at (A) : 9.551999 -2.846001 44.07050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1404776 0.5533088 midg,1,midg; midg,igrid,midg 1.9454692E-02 8.6891487E-02 1,midg,midg; igrid,midg,midg -0.2831570 -0.3493043 gauss-seidel spectral radius is 0.9992301 estimated iterations to convergence 284 setup time was (sec) 1.310000 now iterating at: 17:04:12 rms-change max change #iterations 10.86788 391.7199 at 10iterations 6.432212 164.7429 at 20iterations 3.778872 80.23162 at 30iterations 2.200057 45.49063 at 40iterations 1.276465 24.30187 at 50iterations 0.7367941 14.58671 at 60iterations 0.4246471 8.858795 at 70iterations 0.2434832 5.019267 at 80iterations 0.1398257 2.582746 at 90iterations 8.0045603E-02 1.442850 at 100iterations 4.5710713E-02 0.9188881 at 110iterations 2.6170215E-02 0.4781189 at 120iterations 1.4936642E-02 0.3019152 at 130iterations 8.5196821E-03 0.1581278 at 140iterations 4.8610219E-03 9.2029572E-02 at 150iterations 2.7649649E-03 5.6329727E-02 at 160iterations 1.5721871E-03 2.8987885E-02 at 170iterations 8.9636579E-04 1.6683578E-02 at 180iterations finished qdiffx linear iterations at : 17:04:24 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 8.9636579E-04 1.6683578E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 17:04:25 13.348u 0.224s 0:14.35 94.4% 0+0k 0+0io 0pf+0w