Sun Oct 9 16:02:55 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 Sun Oct 9 2011 at 16:02:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: MG9 970 has a net charge of 1.4000 !!! WARNING: MG9 971 has a net charge of 1.4000 !!! WARNING: MG9 972 has a net charge of 1.4000 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: 0.6294090 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 0.6294090 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2901 net assigned charge : 2.700014 assigned positive charge : 455.0972 centred at (gu) : 90.50433 91.41219 88.64869 assigned negative charge : -452.3987 centred at (gu) : 90.55432 91.51586 88.59515 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8035 nv = 96 ne = 84 npr = 62317 no. pairs analyzed = 62317 no. exposed pairs = 3717 no. arc points = 26328 no. surface atoms = 1261 nbur = 1784 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 4462 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2551 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1437704E-09 6.3716934E-09 midg,1,midg; midg,igrid,midg 9.9353503E-09 -1.0249484E-08 1,midg,midg; igrid,midg,midg 7.3275115E-09 -2.1611481E-09 gauss-seidel spectral radius is 0.9869642 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 16:02:55 rms-change max change #iterations 0.1493350 20.84094 at 10iterations 1.4671180E-02 1.819218 at 20iterations 1.6237962E-03 0.2728806 at 30iterations 3.5106434E-04 6.9038391E-02 at 40iterations 1.2246377E-04 2.5566101E-02 at 50iterations finished qdiffx linear iterations at : 16:02:58 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.2246377E-04 2.5566101E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 16:02:58 3.184u 0.179s 0:03.67 91.2% 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 Sun Oct 9 2011 at 16:02:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: MG9 970 has a net charge of 1.4000 !!! WARNING: MG9 971 has a net charge of 1.4000 !!! WARNING: MG9 972 has a net charge of 1.4000 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: 1.888227 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 1.888227 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2901 net assigned charge : 2.700014 assigned positive charge : 455.0972 centred at (gu) : 91.51232 94.23596 85.94527 assigned negative charge : -452.3987 centred at (gu) : 91.66286 94.54758 85.78536 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26328 grid for indexing accessible points = 1.400000 m= 31053 mr = 60983 m= 5017 mr = 22703 m= 283 mr = 2986 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 36843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22754 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) : 0.6294090 object centre at (A) : 10.62800 30.01750 -6.367499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4232096E-02 2.4660751E-02 midg,1,midg; midg,igrid,midg -4.9936813E-03 -1.2152204E-02 1,midg,midg; igrid,midg,midg -4.3105725E-03 -1.1573413E-02 gauss-seidel spectral radius is 0.9986510 estimated iterations to convergence 216 setup time was (sec) 0.8700000 now iterating at: 16:02:59 rms-change max change #iterations 4.589948 186.3450 at 10iterations 2.152923 79.94308 at 20iterations 1.014151 31.44859 at 30iterations 0.4749747 13.91527 at 40iterations 0.2244485 6.617390 at 50iterations 0.1052368 3.421849 at 60iterations 4.9467735E-02 1.549734 at 70iterations 2.3391010E-02 0.6738701 at 80iterations 1.1031006E-02 0.3291175 at 90iterations 5.2646836E-03 0.1670370 at 100iterations 2.5401141E-03 9.0700150E-02 at 110iterations 1.2557377E-03 4.3640137E-02 at 120iterations finished qdiffx linear iterations at : 16:03:06 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 1.2557377E-03 4.3640137E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 16:03:06 7.415u 0.209s 0:08.10 93.9% 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 Sun Oct 9 2011 at 16:03:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: MG9 970 has a net charge of 1.4000 !!! WARNING: MG9 971 has a net charge of 1.4000 !!! WARNING: MG9 972 has a net charge of 1.4000 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: 2.832340 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 2.832340 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2901 net assigned charge : 2.700014 assigned positive charge : 455.0972 centred at (gu) : 92.26841 96.35366 83.91787 assigned negative charge : -452.3987 centred at (gu) : 92.49439 96.82144 83.67805 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 202509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26328 grid for indexing accessible points = 1.400000 m= 100757 mr = 148568 m= 36452 mr = 82006 m= 8962 mr = 28995 m= 1258 mr = 6592 m= 65 mr = 776 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.500000 number of dielectric boundary points 83044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 23207 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) : 1.888227 object centre at (A) : 10.62800 30.01750 -6.367499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2120789 0.3931475 midg,1,midg; midg,igrid,midg -0.2216216 -0.1168477 1,midg,midg; igrid,midg,midg -0.1473887 -0.1054928 gauss-seidel spectral radius is 0.9992711 estimated iterations to convergence 292 setup time was (sec) 1.800000 now iterating at: 16:03:09 rms-change max change #iterations 10.82642 372.9653 at 10iterations 6.367380 131.0175 at 20iterations 3.723052 76.86275 at 30iterations 2.175230 44.69027 at 40iterations 1.262135 26.46346 at 50iterations 0.7350256 13.40097 at 60iterations 0.4264325 7.411751 at 70iterations 0.2465662 5.319933 at 80iterations 0.1434148 2.767925 at 90iterations 8.2761690E-02 1.408711 at 100iterations 4.7909036E-02 0.8009796 at 110iterations 2.7721250E-02 0.4689140 at 120iterations 1.6070405E-02 0.2814479 at 130iterations 9.3234172E-03 0.1616631 at 140iterations 5.4465863E-03 0.1059647 at 150iterations 3.2086878E-03 6.3474655E-02 at 160iterations 1.9265375E-03 4.5120239E-02 at 170iterations 1.1999683E-03 2.5127411E-02 at 180iterations finished qdiffx linear iterations at : 16:03:19 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 1.1999683E-03 2.5127411E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 16:03:19 12.351u 0.222s 0:12.92 97.2% 0+0k 0+0io 0pf+0w