Mon Oct 10 17:03:22 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 17:03:22 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 !!! WARNING: HIT 111 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5826323 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): -11.33200 49.77000 ymin,ymax (A): -7.433000 41.45000 zmin,zma (A): 0.4030000 56.27800 x,y,z range (A): 61.10200 48.88300 55.87500 scale (grids/A): 0.5826323 object centre (A): 19.21900 17.00850 28.34050 number of atom coordinates read : 3016 total number of charged atoms : 2873 net assigned charge : -4.485972 assigned positive charge : 457.7117 centred at (gu) : 89.98441 89.44587 88.55693 assigned negative charge : -462.1991 centred at (gu) : 89.92873 89.33827 88.50231 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 6725 nv = 96 ne = 84 npr = 60213 no. pairs analyzed = 60213 no. exposed pairs = 4045 no. arc points = 28699 no. surface atoms = 1367 nbur = 1649 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 = 1.484000 m= 298 mr = 3342 m= 2 mr = 16 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 0.4400000 number of dielectric boundary points 3667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2910 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 8602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3647871E-09 2.1590602E-10 midg,1,midg; midg,igrid,midg -4.2651527E-09 1.4109069E-09 1,midg,midg; igrid,midg,midg -2.4350235E-09 3.4594866E-10 gauss-seidel spectral radius is 0.9848028 estimated iterations to convergence 67 setup time was (sec) 0.7500000 now iterating at: 17:03:23 rms-change max change #iterations 0.1010356 17.20199 at 10iterations 7.9880618E-03 1.155086 at 20iterations 6.4451428E-04 9.5535278E-02 at 30iterations 5.3852811E-05 9.0112686E-03 at 40iterations 6.3810171E-06 1.4171600E-03 at 50iterations finished qdiffx linear iterations at : 17:03:27 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 6.3810171E-06 1.4171600E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 17:03:28 4.353u 0.208s 0:05.30 85.8% 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 17:03:28 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 !!! WARNING: HIT 111 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.747897 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): -11.33200 49.77000 ymin,ymax (A): -7.433000 41.45000 zmin,zma (A): 0.4030000 56.27800 x,y,z range (A): 61.10200 48.88300 55.87500 scale (grids/A): 1.747897 object centre (A): 19.21900 17.00850 28.34050 number of atom coordinates read : 3016 total number of charged atoms : 2873 net assigned charge : -4.485972 assigned positive charge : 457.7117 centred at (gu) : 89.95268 88.33673 85.66998 assigned negative charge : -462.1991 centred at (gu) : 89.78587 88.01440 85.50661 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 73534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28699 grid for indexing accessible points = 1.400000 m= 22937 mr = 48426 m= 2701 mr = 15683 m= 96 mr = 1326 m= 0 mr = 11 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 774 time to turn everything in is 0.6800000 number of dielectric boundary points 33822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 22348 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) : 0.5826323 object centre at (A) : 19.21900 17.00850 28.34050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8699533E-03 -1.4071725E-03 midg,1,midg; midg,igrid,midg -1.7455045E-02 4.6335896E-03 1,midg,midg; igrid,midg,midg -3.4964476E-02 1.0409663E-02 gauss-seidel spectral radius is 0.9984327 estimated iterations to convergence 200 setup time was (sec) 1.030000 now iterating at: 17:03:29 rms-change max change #iterations 3.959711 203.7620 at 10iterations 1.742341 66.68230 at 20iterations 0.7747545 29.10857 at 30iterations 0.3430656 11.85405 at 40iterations 0.1511755 4.966690 at 50iterations 6.7128167E-02 2.352417 at 60iterations 2.9677773E-02 1.011948 at 70iterations 1.3156285E-02 0.4392447 at 80iterations 5.8325231E-03 0.2088127 at 90iterations 2.5912779E-03 8.9469910E-02 at 100iterations 1.1521168E-03 4.1515350E-02 at 110iterations 5.1187526E-04 1.7477036E-02 at 120iterations finished qdiffx linear iterations at : 17:03:37 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 5.1187526E-04 1.7477036E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 17:03:39 9.508u 0.262s 0:11.56 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 17:03:39 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 !!! WARNING: HIT 111 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.621845 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): -11.33200 49.77000 ymin,ymax (A): -7.433000 41.45000 zmin,zma (A): 0.4030000 56.27800 x,y,z range (A): 61.10200 48.88300 55.87500 scale (grids/A): 2.621845 object centre (A): 19.21900 17.00850 28.34050 number of atom coordinates read : 3016 total number of charged atoms : 2873 net assigned charge : -4.485972 assigned positive charge : 457.7117 centred at (gu) : 89.92862 87.50481 83.50484 assigned negative charge : -462.1991 centred at (gu) : 89.67883 87.02141 83.25983 start vw surface at 0.2000000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 170456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28699 grid for indexing accessible points = 1.400000 m= 77854 mr = 118844 m= 23656 mr = 60590 m= 4267 mr = 17874 m= 375 mr = 2808 m= 4 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 2430 time to turn everything in is 1.640000 number of dielectric boundary points 76343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 22980 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) : 1.747897 object centre at (A) : 19.21900 17.00850 28.34050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2268721 -0.1014927 midg,1,midg; midg,igrid,midg -0.1787713 7.9747371E-02 1,midg,midg; igrid,midg,midg -0.4339850 0.2331823 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 2.020000 now iterating at: 17:03:42 rms-change max change #iterations 9.972370 329.2485 at 10iterations 5.822505 176.5233 at 20iterations 3.362742 73.40634 at 30iterations 1.931603 44.34968 at 40iterations 1.108251 23.67294 at 50iterations 0.6341833 13.16193 at 60iterations 0.3612628 9.463672 at 70iterations 0.2057181 4.839088 at 80iterations 0.1171350 2.445555 at 90iterations 6.6522866E-02 1.489464 at 100iterations 3.7905972E-02 0.7882376 at 110iterations 2.1481078E-02 0.4103489 at 120iterations 1.2180038E-02 0.2439117 at 130iterations 6.9126044E-03 0.1483841 at 140iterations 3.9111306E-03 8.0650330E-02 at 150iterations 2.2192486E-03 4.3735504E-02 at 160iterations 1.2602253E-03 2.4559021E-02 at 170iterations 7.1412319E-04 1.3383627E-02 at 180iterations finished qdiffx linear iterations at : 17:03:55 total time elapsed so far: 15.21000 # loops : 180 mean,max change (kT/e) : 7.1412319E-04 1.3383627E-02 energy calculations done at 15.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.45000 DelPhi exited at 17:03:56 15.454u 0.247s 0:16.29 96.3% 0+0k 0+0io 0pf+0w