Sun Feb 12 05:09:20 PST 2012 #!/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_thin.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 Sun Feb 12 2012 at 05:09:21 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5767330 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 0.5767330 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3142 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 91.10113 89.94644 90.15296 assigned negative charge : -457.5339 centred at (gu) : 91.22202 89.92796 90.26438 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6640 nv = 96 ne = 84 npr = 68433 no. pairs analyzed = 68433 no. exposed pairs = 3743 no. arc points = 26358 no. surface atoms = 1258 nbur = 1884 mkacc time = 0.1200000 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 = 1.512000 m= 293 mr = 3629 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2694 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6107991E-09 -1.8854243E-09 midg,1,midg; midg,igrid,midg 1.0051684E-10 8.3943869E-10 1,midg,midg; igrid,midg,midg 2.2315063E-09 -2.6354541E-09 gauss-seidel spectral radius is 0.9844909 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 05:09:21 rms-change max change #iterations 9.8413929E-02 16.62820 at 10iterations 7.9532424E-03 1.243216 at 20iterations 1.1798056E-03 0.2411137 at 30iterations 4.5134171E-04 0.1014042 at 40iterations 1.9807732E-04 4.4672012E-02 at 50iterations finished qdiffx linear iterations at : 05:09:27 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.9807732E-04 4.4672012E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 05:09:27 3.545u 0.219s 0:06.62 56.6% 0+0k 0+0io 6pf+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 Sun Feb 12 2012 at 05:09:27 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.730199 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 1.730199 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3142 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 93.30260 89.83813 90.45805 assigned negative charge : -457.5339 centred at (gu) : 93.66559 89.78358 90.79282 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26358 grid for indexing accessible points = 1.400000 m= 23166 mr = 51374 m= 2591 mr = 16334 m= 83 mr = 1374 m= 0 mr = 7 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 702 time to turn everything in is 0.3600000 number of dielectric boundary points 30600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 22596 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) : 0.5767330 object centre at (A) : 1.770501 -0.7205009 22.12450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3267033E-02 1.9956194E-02 midg,1,midg; midg,igrid,midg -5.5257772E-04 1.4303211E-03 1,midg,midg; igrid,midg,midg 4.2711264E-03 -8.6834449E-03 gauss-seidel spectral radius is 0.9984011 estimated iterations to convergence 198 setup time was (sec) 0.5900000 now iterating at: 05:09:28 rms-change max change #iterations 3.833816 188.5242 at 10iterations 1.680990 54.41241 at 20iterations 0.7386010 26.54895 at 30iterations 0.3261436 11.59628 at 40iterations 0.1438380 5.081652 at 50iterations 6.3262448E-02 2.130798 at 60iterations 2.8038530E-02 1.051573 at 70iterations 1.2523689E-02 0.4083519 at 80iterations 5.7599358E-03 0.2618885 at 90iterations 2.8646307E-03 0.1113358 at 100iterations 1.5979671E-03 6.6138268E-02 at 110iterations 1.0328364E-03 4.4151306E-02 at 120iterations finished qdiffx linear iterations at : 05:09:41 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.0328364E-03 4.4151306E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 05:09:42 7.992u 0.216s 0:14.72 55.7% 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 Sun Feb 12 2012 at 05:09:42 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.595299 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 2.595299 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3142 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 94.95368 89.75690 90.68674 assigned negative charge : -457.5339 centred at (gu) : 95.49839 89.67529 91.18927 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 171558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26358 grid for indexing accessible points = 1.400000 m= 80356 mr = 125199 m= 23590 mr = 64779 m= 4264 mr = 18025 m= 365 mr = 2903 m= 5 mr = 174 m= 0 mr = 3 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 2343 time to turn everything in is 0.9000000 number of dielectric boundary points 69055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 23298 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) : 1.730199 object centre at (A) : 1.770501 -0.7205009 22.12450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0039480E-02 0.5349548 midg,1,midg; midg,igrid,midg -7.8905839E-03 2.0994248E-02 1,midg,midg; igrid,midg,midg 2.1091990E-02 -9.6406877E-02 gauss-seidel spectral radius is 0.9992006 estimated iterations to convergence 279 setup time was (sec) 1.150000 now iterating at: 05:09:45 rms-change max change #iterations 9.459273 322.3915 at 10iterations 5.381986 129.9805 at 20iterations 3.068578 70.59869 at 30iterations 1.737596 38.28451 at 40iterations 0.9816681 23.30813 at 50iterations 0.5530220 10.70146 at 60iterations 0.3120793 6.664897 at 70iterations 0.1760674 3.503139 at 80iterations 9.9376306E-02 1.853100 at 90iterations 5.5973575E-02 1.157951 at 100iterations 3.1591196E-02 0.5935311 at 110iterations 1.7885806E-02 0.3589048 at 120iterations 1.0191025E-02 0.2089748 at 130iterations 5.9117689E-03 0.1317711 at 140iterations 3.5328467E-03 8.3372116E-02 at 150iterations 2.2429740E-03 6.0470581E-02 at 160iterations 1.5357736E-03 3.9249420E-02 at 170iterations 1.1375572E-03 2.9382706E-02 at 180iterations finished qdiffx linear iterations at : 05:10:08 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 1.1375572E-03 2.9382706E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 05:10:09 13.274u 0.237s 0:27.38 49.3% 0+0k 0+0io 0pf+0w