Mon Oct 10 13:54:24 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 Mon Oct 10 2011 at 13:54:24 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4996 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5549666 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): 3.189000 65.00800 ymin,ymax (A): -8.794000 53.52900 zmin,zma (A): -2.167000 61.98100 x,y,z range (A): 61.81900 62.32300 64.14800 scale (grids/A): 0.5549666 object centre (A): 34.09850 22.36750 29.90700 number of atom coordinates read : 4996 total number of charged atoms : 4868 net assigned charge : 2.621037 assigned positive charge : 769.5186 centred at (gu) : 88.49506 89.19365 89.37487 assigned negative charge : -766.9036 centred at (gu) : 88.37081 89.22186 89.37599 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10060 nv = 96 ne = 84 npr = 100325 no. pairs analyzed = 100325 no. exposed pairs = 5832 no. arc points = 39191 no. surface atoms = 1986 nbur = 3010 mkacc time = 0.1700000 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= 478 mr = 5778 m= 4 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4050 ## 436 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 13148 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2269390E-10 2.0895689E-10 midg,1,midg; midg,igrid,midg 8.6161545E-10 -1.5386199E-10 1,midg,midg; igrid,midg,midg -2.5513212E-09 1.5258933E-09 gauss-seidel spectral radius is 0.9834018 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 13:54:24 rms-change max change #iterations 0.1095365 15.59046 at 10iterations 1.0416125E-02 1.462404 at 20iterations 3.2228020E-03 0.3333292 at 30iterations 1.5565854E-03 0.1736355 at 40iterations 7.7723101E-04 8.9789391E-02 at 50iterations finished qdiffx linear iterations at : 13:54:27 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 7.7723101E-04 8.9789391E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 13:54:28 3.655u 0.163s 0:04.66 81.7% 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 13:54:28 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4996 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.664900 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): 3.189000 65.00800 ymin,ymax (A): -8.794000 53.52900 zmin,zma (A): -2.167000 61.98100 x,y,z range (A): 61.81900 62.32300 64.14800 scale (grids/A): 1.664900 object centre (A): 34.09850 22.36750 29.90700 number of atom coordinates read : 4996 total number of charged atoms : 4868 net assigned charge : 2.621037 assigned positive charge : 769.5186 centred at (gu) : 85.48380 87.57925 88.12292 assigned negative charge : -766.9036 centred at (gu) : 85.11248 87.66574 88.12804 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 111895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39191 grid for indexing accessible points = 1.400000 m= 40014 mr = 81418 m= 4973 mr = 29181 m= 183 mr = 2722 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 188 time to turn everything in is 0.5400000 number of dielectric boundary points 43721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 371 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 37411 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) : 0.5549666 object centre at (A) : 34.09850 22.36750 29.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0142991E-02 -2.8606597E-02 midg,1,midg; midg,igrid,midg 2.2148896E-02 9.5855696E-03 1,midg,midg; igrid,midg,midg -1.9905778E-02 3.6602531E-02 gauss-seidel spectral radius is 0.9984419 estimated iterations to convergence 201 setup time was (sec) 0.7600000 now iterating at: 13:54:29 rms-change max change #iterations 4.812345 218.6950 at 10iterations 2.139183 64.96686 at 20iterations 0.9520680 27.23213 at 30iterations 0.4239767 11.43575 at 40iterations 0.1891212 5.242757 at 50iterations 8.5117370E-02 2.491253 at 60iterations 3.8818926E-02 1.075632 at 70iterations 1.8244127E-02 0.5222702 at 80iterations 9.4125494E-03 0.2710876 at 90iterations 5.5795768E-03 0.1614037 at 100iterations 3.7825329E-03 9.6115112E-02 at 110iterations 2.7984672E-03 6.7555428E-02 at 120iterations finished qdiffx linear iterations at : 13:54:37 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 2.7984672E-03 6.7555428E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 13:54:37 8.200u 0.220s 0:08.75 96.2% 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 13:54:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4996 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.497350 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): 3.189000 65.00800 ymin,ymax (A): -8.794000 53.52900 zmin,zma (A): -2.167000 61.98100 x,y,z range (A): 61.81900 62.32300 64.14800 scale (grids/A): 2.497350 object centre (A): 34.09850 22.36750 29.90700 number of atom coordinates read : 4996 total number of charged atoms : 4868 net assigned charge : 2.621037 assigned positive charge : 769.5186 centred at (gu) : 83.22532 86.36863 87.18401 assigned negative charge : -766.9036 centred at (gu) : 82.66863 86.49854 87.19196 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 259983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39191 grid for indexing accessible points = 1.400000 m= 133212 mr = 197600 m= 43802 mr = 109140 m= 8222 mr = 34463 m= 745 mr = 5689 m= 19 mr = 396 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 722 time to turn everything in is 1.350000 number of dielectric boundary points 98695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 38919 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) : 1.664900 object centre at (A) : 34.09850 22.36750 29.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3520189 -0.6663688 midg,1,midg; midg,igrid,midg 8.3670288E-02 -3.2925070E-03 1,midg,midg; igrid,midg,midg -0.4040692 0.5118853 gauss-seidel spectral radius is 0.9992563 estimated iterations to convergence 289 setup time was (sec) 1.590000 now iterating at: 13:54:39 rms-change max change #iterations 12.19502 338.9157 at 10iterations 7.203074 166.4298 at 20iterations 4.227066 79.61862 at 30iterations 2.471546 45.75117 at 40iterations 1.440435 25.45510 at 50iterations 0.8354515 14.22488 at 60iterations 0.4842435 8.331234 at 70iterations 0.2804233 4.905342 at 80iterations 0.1624901 2.686051 at 90iterations 9.3885556E-02 1.536001 at 100iterations 5.4493163E-02 0.9360218 at 110iterations 3.1799112E-02 0.4928679 at 120iterations 1.8789047E-02 0.2927742 at 130iterations 1.1404851E-02 0.1843357 at 140iterations 7.2508682E-03 0.1181822 at 150iterations 4.9318052E-03 8.4938049E-02 at 160iterations 3.6267813E-03 5.9078217E-02 at 170iterations 2.8418440E-03 4.3703079E-02 at 180iterations finished qdiffx linear iterations at : 13:54:51 total time elapsed so far: 13.48000 # loops : 180 mean,max change (kT/e) : 2.8418440E-03 4.3703079E-02 energy calculations done at 13.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 13:54:52 13.616u 0.230s 0:14.53 95.2% 0+0k 0+0io 0pf+0w