Sat Oct 8 17:00:23 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 Sat Oct 8 2011 at 17:00:23 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3629 !!! WARNING: ASL 237 has a net charge of -0.1000 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: 0.5397211 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): 20.80400 83.99400 ymin,ymax (A): -18.05200 40.04700 zmin,zma (A): 77.68200 143.6420 x,y,z range (A): 63.18999 58.09900 65.96000 scale (grids/A): 0.5397211 object centre (A): 52.39900 10.99750 110.6620 number of atom coordinates read : 3629 total number of charged atoms : 3481 net assigned charge : -7.099971 assigned positive charge : 554.1728 centred at (gu) : 89.71505 90.47835 90.18436 assigned negative charge : -561.2748 centred at (gu) : 89.77697 90.45953 90.17288 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6643 nv = 96 ne = 84 npr = 74554 no. pairs analyzed = 74554 no. exposed pairs = 4657 no. arc points = 31168 no. surface atoms = 1562 nbur = 2067 mkacc time = 0.1600000 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 = 1.596000 m= 272 mr = 3450 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3101 ## 359 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8851 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0474243E-10 -2.8361480E-10 midg,1,midg; midg,igrid,midg -4.1998865E-10 -2.4961624E-10 1,midg,midg; igrid,midg,midg 6.5524690E-11 -7.0870487E-10 gauss-seidel spectral radius is 0.9823467 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 17:00:24 rms-change max change #iterations 7.8483023E-02 12.99722 at 10iterations 5.2038049E-03 0.7844009 at 20iterations 4.4226379E-04 7.0104599E-02 at 30iterations 9.2503076E-05 1.5241623E-02 at 40iterations 2.9443305E-05 4.4784546E-03 at 50iterations finished qdiffx linear iterations at : 17:00:27 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 2.9443305E-05 4.4784546E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 17:00:27 3.182u 0.152s 0:03.66 90.9% 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 Sat Oct 8 2011 at 17:00:27 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 # of charge parameter records: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3629 !!! WARNING: ASL 237 has a net charge of -0.1000 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: 1.619163 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): 20.80400 83.99400 ymin,ymax (A): -18.05200 40.04700 zmin,zma (A): 77.68200 143.6420 x,y,z range (A): 63.18999 58.09900 65.96000 scale (grids/A): 1.619163 object centre (A): 52.39900 10.99750 110.6620 number of atom coordinates read : 3629 total number of charged atoms : 3481 net assigned charge : -7.099971 assigned positive charge : 554.1728 centred at (gu) : 89.14407 91.43398 90.55196 assigned negative charge : -561.2748 centred at (gu) : 89.33057 91.37794 90.51827 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31168 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23274 mr = 50255 m= 2400 mr = 15788 m= 54 mr = 1081 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 32109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 26579 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) : 0.5397211 object centre at (A) : 52.39900 10.99750 110.6620 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8418532E-03 -1.5664296E-04 midg,1,midg; midg,igrid,midg -4.1901930E-03 9.8098442E-04 1,midg,midg; igrid,midg,midg -1.0235283E-02 -2.7818179E-02 gauss-seidel spectral radius is 0.9982095 estimated iterations to convergence 188 setup time was (sec) 0.8000000 now iterating at: 17:00:28 rms-change max change #iterations 3.713910 167.6243 at 10iterations 1.555341 57.83789 at 20iterations 0.6523918 26.38562 at 30iterations 0.2742977 9.776562 at 40iterations 0.1158086 4.345112 at 50iterations 4.8535924E-02 1.717813 at 60iterations 2.0548455E-02 0.7170686 at 70iterations 8.7410333E-03 0.2961102 at 80iterations 3.7714632E-03 0.1406913 at 90iterations 1.6865821E-03 5.5490494E-02 at 100iterations 8.1075903E-04 3.0853271E-02 at 110iterations 4.3406262E-04 1.4244318E-02 at 120iterations finished qdiffx linear iterations at : 17:00:34 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 4.3406262E-04 1.4244318E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 17:00:35 7.061u 0.155s 0:07.49 96.2% 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 Sat Oct 8 2011 at 17:00:35 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3629 !!! WARNING: ASL 237 has a net charge of -0.1000 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: 2.428745 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): 20.80400 83.99400 ymin,ymax (A): -18.05200 40.04700 zmin,zma (A): 77.68200 143.6420 x,y,z range (A): 63.18999 58.09900 65.96000 scale (grids/A): 2.428745 object centre (A): 52.39900 10.99750 110.6620 number of atom coordinates read : 3629 total number of charged atoms : 3481 net assigned charge : -7.099971 assigned positive charge : 554.1728 centred at (gu) : 88.71592 92.15063 90.82780 assigned negative charge : -561.2748 centred at (gu) : 88.99583 92.06673 90.77732 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 170590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31168 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 80060 mr = 123038 m= 22890 mr = 62499 m= 3755 mr = 17047 m= 226 mr = 2297 m= 9 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 72581 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 27809 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) : 1.619163 object centre at (A) : 52.39900 10.99750 110.6620 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2215954E-03 1.5027539E-04 midg,1,midg; midg,igrid,midg -9.0615429E-02 1.5533307E-03 1,midg,midg; igrid,midg,midg -0.2542419 -0.4021560 gauss-seidel spectral radius is 0.9991562 estimated iterations to convergence 272 setup time was (sec) 1.540000 now iterating at: 17:00:36 rms-change max change #iterations 9.751513 338.7318 at 10iterations 5.538387 134.2396 at 20iterations 3.138813 77.57318 at 30iterations 1.764244 36.55244 at 40iterations 0.9863703 19.97808 at 50iterations 0.5507413 10.56709 at 60iterations 0.3073083 6.444923 at 70iterations 0.1710124 3.672440 at 80iterations 9.5106810E-02 1.809435 at 90iterations 5.2761283E-02 0.9778061 at 100iterations 2.9306095E-02 0.6375332 at 110iterations 1.6234815E-02 0.3148565 at 120iterations 8.9894049E-03 0.1579351 at 130iterations 4.9939384E-03 9.3214035E-02 at 140iterations 2.7656436E-03 5.1855087E-02 at 150iterations 1.5358176E-03 2.8457642E-02 at 160iterations 8.5307768E-04 1.5767574E-02 at 170iterations 4.7622001E-04 9.3846917E-03 at 180iterations finished qdiffx linear iterations at : 17:00:46 total time elapsed so far: 11.01000 # loops : 180 mean,max change (kT/e) : 4.7622001E-04 9.3846917E-03 energy calculations done at 11.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.18000 DelPhi exited at 17:00:46 11.186u 0.177s 0:11.68 97.1% 0+0k 0+0io 0pf+0w