Mon Oct 10 21:11:30 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 21:11:30 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 !!! WARNING: HIR 323 has a net charge of 0.5140 !!! WARNING: HIR 449 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6783795 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): -22.46800 26.79100 ymin,ymax (A): 2.541000 46.31000 zmin,zma (A): -2.276000 50.20200 x,y,z range (A): 49.25900 43.76900 52.47800 scale (grids/A): 0.6783795 object centre (A): 2.161500 24.42550 23.96300 number of atom coordinates read : 2443 total number of charged atoms : 2309 net assigned charge : -0.9719919 assigned positive charge : 358.0811 centred at (gu) : 90.88676 91.55805 91.01869 assigned negative charge : -359.0540 centred at (gu) : 90.82994 91.46052 91.03882 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 50418 no. pairs analyzed = 50418 no. exposed pairs = 3313 no. arc points = 22591 no. surface atoms = 1114 nbur = 1329 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 478 mr = 4006 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2053 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5536790E-10 -1.2777017E-08 midg,1,midg; midg,igrid,midg -2.3994508E-08 3.2345554E-08 1,midg,midg; igrid,midg,midg -1.7562437E-08 1.4152249E-08 gauss-seidel spectral radius is 0.9887245 estimated iterations to convergence 77 setup time was (sec) 0.6400000 now iterating at: 21:11:31 rms-change max change #iterations 0.1809168 24.63273 at 10iterations 2.0014348E-02 2.944405 at 20iterations 2.3321779E-03 0.3473701 at 30iterations 2.7731381E-04 4.0077925E-02 at 40iterations 3.8530441E-05 5.0344467E-03 at 50iterations finished qdiffx linear iterations at : 21:11:34 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 3.8530441E-05 5.0344467E-03 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.960000 DelPhi exited at 21:11:35 3.967u 0.177s 0:04.75 86.9% 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 21:11:35 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 !!! WARNING: HIR 323 has a net charge of 0.5140 !!! WARNING: HIR 449 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.035139 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): -22.46800 26.79100 ymin,ymax (A): 2.541000 46.31000 zmin,zma (A): -2.276000 50.20200 x,y,z range (A): 49.25900 43.76900 52.47800 scale (grids/A): 2.035139 object centre (A): 2.161500 24.42550 23.96300 number of atom coordinates read : 2443 total number of charged atoms : 2309 net assigned charge : -0.9719919 assigned positive charge : 358.0811 centred at (gu) : 92.65961 94.67387 93.05553 assigned negative charge : -359.0540 centred at (gu) : 92.48991 94.38154 93.11658 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 81254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22591 grid for indexing accessible points = 1.400000 m= 30660 mr = 55418 m= 5902 mr = 22109 m= 437 mr = 3705 m= 10 mr = 140 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 36892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 18296 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) : 0.6783795 object centre at (A) : 2.161500 24.42550 23.96300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3297744E-02 -6.4118947E-03 midg,1,midg; midg,igrid,midg -1.7177580E-02 2.2837918E-03 1,midg,midg; igrid,midg,midg 8.0372784E-03 2.5174757E-02 gauss-seidel spectral radius is 0.9987857 estimated iterations to convergence 227 setup time was (sec) 1.190000 now iterating at: 21:11:37 rms-change max change #iterations 4.620061 177.0138 at 10iterations 2.251881 75.81195 at 20iterations 1.097467 32.16380 at 30iterations 0.5383994 16.48371 at 40iterations 0.2619359 7.993470 at 50iterations 0.1280320 3.576028 at 60iterations 6.2700279E-02 1.843304 at 70iterations 3.0537199E-02 0.8613656 at 80iterations 1.4934506E-02 0.4731560 at 90iterations 7.3046209E-03 0.2292337 at 100iterations 3.5938062E-03 0.1159248 at 110iterations 1.7624011E-03 5.1475525E-02 at 120iterations finished qdiffx linear iterations at : 21:11:45 total time elapsed so far: 9.730000 # loops : 120 mean,max change (kT/e) : 1.7624011E-03 5.1475525E-02 energy calculations done at 9.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.960000 DelPhi exited at 21:11:46 9.963u 0.275s 0:10.54 97.0% 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 21:11:46 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 !!! WARNING: HIR 323 has a net charge of 0.5140 !!! WARNING: HIR 449 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.052708 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): -22.46800 26.79100 ymin,ymax (A): 2.541000 46.31000 zmin,zma (A): -2.276000 50.20200 x,y,z range (A): 49.25900 43.76900 52.47800 scale (grids/A): 3.052708 object centre (A): 2.161500 24.42550 23.96300 number of atom coordinates read : 2443 total number of charged atoms : 2309 net assigned charge : -0.9719919 assigned positive charge : 358.0811 centred at (gu) : 93.98923 97.01083 94.58316 assigned negative charge : -359.0540 centred at (gu) : 93.73490 96.57225 94.67466 start vw surface at 0.1800000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 187914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22591 grid for indexing accessible points = 1.400000 m= 95425 mr = 134919 m= 38550 mr = 76820 m= 10927 mr = 30560 m= 1912 mr = 8144 m= 95 mr = 1267 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 83084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 18472 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) : 2.035139 object centre at (A) : 2.161500 24.42550 23.96300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3514353E-02 -0.1252398 midg,1,midg; midg,igrid,midg -0.1528452 -0.1132777 1,midg,midg; igrid,midg,midg 0.2280984 0.2995302 gauss-seidel spectral radius is 0.9993070 estimated iterations to convergence 300 setup time was (sec) 2.440000 now iterating at: 21:11:48 rms-change max change #iterations 10.75486 410.1638 at 10iterations 6.460711 166.0930 at 20iterations 3.858636 77.52150 at 30iterations 2.294946 51.27281 at 40iterations 1.356910 26.55104 at 50iterations 0.8020845 15.12958 at 60iterations 0.4725969 8.209328 at 70iterations 0.2785107 4.811821 at 80iterations 0.1637989 2.719122 at 90iterations 9.6086100E-02 1.562347 at 100iterations 5.6456711E-02 0.9489155 at 110iterations 3.3005271E-02 0.5523090 at 120iterations 1.9375781E-02 0.3402338 at 130iterations 1.1380659E-02 0.1962119 at 140iterations 6.6832192E-03 0.1130016 at 150iterations 3.9275442E-03 7.1037292E-02 at 160iterations 2.3211387E-03 3.9950371E-02 at 170iterations 1.3780488E-03 2.4070740E-02 at 180iterations finished qdiffx linear iterations at : 21:12:03 total time elapsed so far: 16.53000 # loops : 180 mean,max change (kT/e) : 1.3780488E-03 2.4070740E-02 energy calculations done at 16.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.77000 DelPhi exited at 21:12:03 16.774u 0.292s 0:17.56 97.1% 0+0k 0+0io 0pf+0w