Tue Oct 11 03:44:48 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 Tue Oct 11 2011 at 03:44:48 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 !!! WARNING: HIQ 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6069803 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): -12.25700 37.18200 ymin,ymax (A): -27.23300 21.39800 zmin,zma (A): -13.20500 45.44600 x,y,z range (A): 49.43900 48.63100 58.65100 scale (grids/A): 0.6069803 object centre (A): 12.46250 -2.917500 16.12050 number of atom coordinates read : 3222 total number of charged atoms : 2801 net assigned charge : -2.320979 assigned positive charge : 451.0053 centred at (gu) : 90.21889 90.99026 92.36232 assigned negative charge : -453.3270 centred at (gu) : 89.97554 90.90591 92.24461 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7117 nv = 96 ne = 84 npr = 60940 no. pairs analyzed = 60940 no. exposed pairs = 3448 no. arc points = 24009 no. surface atoms = 1165 nbur = 2057 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 4069 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3500000 number of dielectric boundary points 3367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2483 ## 287 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5450146E-09 8.0763032E-09 midg,1,midg; midg,igrid,midg -4.7390434E-09 3.6898575E-09 1,midg,midg; igrid,midg,midg -1.3869351E-08 1.1520195E-08 gauss-seidel spectral radius is 0.9859713 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 03:44:49 rms-change max change #iterations 0.1237272 19.16675 at 10iterations 1.1216354E-02 1.543297 at 20iterations 1.1500842E-03 0.1562271 at 30iterations 2.1070508E-04 2.5211334E-02 at 40iterations 5.9799266E-05 8.2492828E-03 at 50iterations finished qdiffx linear iterations at : 03:44:53 total time elapsed so far: 4.570000 # loops : 50 mean,max change (kT/e) : 5.9799266E-05 8.2492828E-03 energy calculations done at 4.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 03:44:53 4.752u 0.380s 0:05.56 92.2% 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 Tue Oct 11 2011 at 03:44:53 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 !!! WARNING: HIQ 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.820941 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): -12.25700 37.18200 ymin,ymax (A): -27.23300 21.39800 zmin,zma (A): -13.20500 45.44600 x,y,z range (A): 49.43900 48.63100 58.65100 scale (grids/A): 1.820941 object centre (A): 12.46250 -2.917500 16.12050 number of atom coordinates read : 3222 total number of charged atoms : 2801 net assigned charge : -2.320979 assigned positive charge : 451.0053 centred at (gu) : 90.65578 92.97025 97.08606 assigned negative charge : -453.3270 centred at (gu) : 89.92621 92.71759 96.73348 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24009 grid for indexing accessible points = 1.400000 m= 27609 mr = 55053 m= 3819 mr = 20717 m= 174 mr = 2254 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2761 time to turn everything in is 0.6400000 number of dielectric boundary points 31032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21830 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) : 0.6069803 object centre at (A) : 12.46250 -2.917500 16.12050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6547645E-02 -2.2862030E-03 midg,1,midg; midg,igrid,midg -1.0543969E-02 -2.0198405E-03 1,midg,midg; igrid,midg,midg -9.7398851E-03 3.7977722E-02 gauss-seidel spectral radius is 0.9985376 estimated iterations to convergence 207 setup time was (sec) 0.9900000 now iterating at: 03:44:55 rms-change max change #iterations 4.263183 193.8565 at 10iterations 1.950294 63.06239 at 20iterations 0.8867015 29.69429 at 30iterations 0.4067394 13.85604 at 40iterations 0.1858415 5.786581 at 50iterations 8.4868319E-02 2.665943 at 60iterations 3.8923513E-02 1.118875 at 70iterations 1.7729271E-02 0.5567232 at 80iterations 8.1308773E-03 0.3000298 at 90iterations 3.7218344E-03 0.1184464 at 100iterations 1.7004408E-03 5.7887435E-02 at 110iterations 7.8000413E-04 2.6779175E-02 at 120iterations finished qdiffx linear iterations at : 03:45:06 total time elapsed so far: 11.87000 # loops : 120 mean,max change (kT/e) : 7.8000413E-04 2.6779175E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 03:45:06 12.044u 0.430s 0:13.05 95.5% 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 Tue Oct 11 2011 at 03:45:07 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 !!! WARNING: HIQ 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.731411 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): -12.25700 37.18200 ymin,ymax (A): -27.23300 21.39800 zmin,zma (A): -13.20500 45.44600 x,y,z range (A): 49.43900 48.63100 58.65100 scale (grids/A): 2.731411 object centre (A): 12.46250 -2.917500 16.12050 number of atom coordinates read : 3222 total number of charged atoms : 2801 net assigned charge : -2.320979 assigned positive charge : 451.0053 centred at (gu) : 90.98354 94.45529 100.6290 assigned negative charge : -453.3270 centred at (gu) : 89.88921 94.07629 100.1000 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 179549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24009 grid for indexing accessible points = 1.400000 m= 91243 mr = 133400 m= 31154 mr = 75664 m= 6568 mr = 25070 m= 789 mr = 4712 m= 29 mr = 495 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 9151 time to turn everything in is 1.640000 number of dielectric boundary points 69986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 22406 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) : 1.820941 object centre at (A) : 12.46250 -2.917500 16.12050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9879424 0.1490221 midg,1,midg; midg,igrid,midg -0.1396319 -7.7358685E-02 1,midg,midg; igrid,midg,midg -9.2997111E-02 0.3711427 gauss-seidel spectral radius is 0.9992306 estimated iterations to convergence 285 setup time was (sec) 1.970000 now iterating at: 03:45:09 rms-change max change #iterations 10.11983 326.8910 at 10iterations 5.843074 151.7766 at 20iterations 3.358905 73.78326 at 30iterations 1.924878 41.67619 at 40iterations 1.100478 28.89228 at 50iterations 0.6293923 11.62435 at 60iterations 0.3590942 6.772084 at 70iterations 0.2051505 3.934046 at 80iterations 0.1168477 2.226448 at 90iterations 6.6565320E-02 1.184683 at 100iterations 3.8046964E-02 0.6749123 at 110iterations 2.1701893E-02 0.4059772 at 120iterations 1.2395145E-02 0.2283478 at 130iterations 7.0693805E-03 0.1295972 at 140iterations 4.0650037E-03 7.8496933E-02 at 150iterations 2.3539225E-03 4.5019150E-02 at 160iterations 1.3815651E-03 2.5688171E-02 at 170iterations 8.2949142E-04 1.5772820E-02 at 180iterations finished qdiffx linear iterations at : 03:45:26 total time elapsed so far: 18.81000 # loops : 180 mean,max change (kT/e) : 8.2949142E-04 1.5772820E-02 energy calculations done at 18.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.98000 DelPhi exited at 03:45:27 18.982u 0.479s 0:20.08 96.8% 0+0k 0+0io 0pf+0w