Tue Nov 22 14:11:36 PST 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 Nov 22 2011 at 14:11:40 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 = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5921687 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): -35.15600 11.15000 ymin,ymax (A): 1.020000 41.79800 zmin,zma (A): -1.288000 58.83000 x,y,z range (A): 46.30600 40.77800 60.11800 scale (grids/A): 0.5921687 object centre (A): -12.00300 21.40900 28.77100 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.7999 centred at (gu) : 90.17575 89.34142 89.44019 assigned negative charge : -290.8002 centred at (gu) : 90.08034 89.48427 89.44217 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4677 nv = 96 ne = 84 npr = 40042 no. pairs analyzed = 40042 no. exposed pairs = 2460 no. arc points = 17136 no. surface atoms = 841 nbur = 1129 mkacc time = 9.0000004E-02 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= 223 mr = 2565 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1778 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1456492E-09 8.1889956E-10 midg,1,midg; midg,igrid,midg 4.6290438E-09 -1.8265229E-09 1,midg,midg; igrid,midg,midg -1.0484362E-09 3.1100822E-09 gauss-seidel spectral radius is 0.9851928 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 14:11:44 rms-change max change #iterations 9.0758175E-02 17.72269 at 10iterations 7.5233458E-03 1.332748 at 20iterations 6.1356189E-04 0.1157641 at 30iterations 4.9972368E-05 9.6945763E-03 at 40iterations 4.0875316E-06 8.7070465E-04 at 50iterations finished qdiffx linear iterations at : 14:11:53 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 4.0875316E-06 8.7070465E-04 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:11:55 3.765u 0.229s 0:15.45 25.7% 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 Nov 22 2011 at 14:11:56 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 = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.776506 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): -35.15600 11.15000 ymin,ymax (A): 1.020000 41.79800 zmin,zma (A): -1.288000 58.83000 x,y,z range (A): 46.30600 40.77800 60.11800 scale (grids/A): 1.776506 object centre (A): -12.00300 21.40900 28.77100 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.7999 centred at (gu) : 90.52686 88.02415 88.32044 assigned negative charge : -290.8002 centred at (gu) : 90.24104 88.45316 88.32661 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 50612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17136 grid for indexing accessible points = 1.400000 m= 17666 mr = 34555 m= 2329 mr = 13176 m= 99 mr = 1387 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 334 time to turn everything in is 0.4100000 number of dielectric boundary points 21562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14316 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) : 0.5921687 object centre at (A) : -12.00300 21.40900 28.77100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0894081E-02 2.2634134E-02 midg,1,midg; midg,igrid,midg 1.9931865E-03 -6.2914304E-03 1,midg,midg; igrid,midg,midg -1.0302679E-03 5.2111421E-04 gauss-seidel spectral radius is 0.9983572 estimated iterations to convergence 196 setup time was (sec) 0.7200000 now iterating at: 14:11:58 rms-change max change #iterations 3.172305 149.2390 at 10iterations 1.375661 61.44036 at 20iterations 0.5983202 27.20072 at 30iterations 0.2601292 10.42476 at 40iterations 0.1129578 4.768730 at 50iterations 4.9053803E-02 1.991966 at 60iterations 2.1342857E-02 0.9179745 at 70iterations 9.2823133E-03 0.3529749 at 80iterations 4.0316847E-03 0.1566467 at 90iterations 1.7568966E-03 7.0276260E-02 at 100iterations 7.6302869E-04 2.9297113E-02 at 110iterations 3.3362198E-04 1.2269020E-02 at 120iterations finished qdiffx linear iterations at : 14:12:15 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 3.3362198E-04 1.2269020E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:12:17 7.780u 0.221s 0:21.00 38.0% 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 Tue Nov 22 2011 at 14:12:18 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 = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.664759 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): -35.15600 11.15000 ymin,ymax (A): 1.020000 41.79800 zmin,zma (A): -1.288000 58.83000 x,y,z range (A): 46.30600 40.77800 60.11800 scale (grids/A): 2.664759 object centre (A): -12.00300 21.40900 28.77100 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 293.7999 centred at (gu) : 90.79025 87.03631 87.48063 assigned negative charge : -290.8002 centred at (gu) : 90.36163 87.67976 87.49005 start vw surface at 0.1200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 117018 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17136 grid for indexing accessible points = 1.400000 m= 57989 mr = 83691 m= 20000 mr = 47612 m= 3923 mr = 16257 m= 443 mr = 2881 m= 19 mr = 262 m= 0 mr = 11 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1151 time to turn everything in is 0.9500000 number of dielectric boundary points 48678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 14702 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) : 1.776506 object centre at (A) : -12.00300 21.40900 28.77100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1873343E-02 0.2103951 midg,1,midg; midg,igrid,midg -1.6799645E-02 -9.6341185E-02 1,midg,midg; igrid,midg,midg -3.8452107E-02 -3.0908149E-02 gauss-seidel spectral radius is 0.9991588 estimated iterations to convergence 272 setup time was (sec) 1.250000 now iterating at: 14:12:25 rms-change max change #iterations 7.702438 326.6615 at 10iterations 4.296852 134.4144 at 20iterations 2.395462 63.74202 at 30iterations 1.326299 30.83104 at 40iterations 0.7320429 15.94756 at 50iterations 0.4058788 9.404888 at 60iterations 0.2236931 4.860806 at 70iterations 0.1239290 2.838203 at 80iterations 6.8307847E-02 1.653370 at 90iterations 3.7822429E-02 0.8425255 at 100iterations 2.0895032E-02 0.4935722 at 110iterations 1.1514908E-02 0.2641850 at 120iterations 6.3622994E-03 0.1522141 at 130iterations 3.5214436E-03 8.2050323E-02 at 140iterations 1.9432396E-03 4.2129159E-02 at 150iterations 1.0734763E-03 2.3233414E-02 at 160iterations 5.9271150E-04 1.2187004E-02 at 170iterations 3.2791839E-04 7.8792572E-03 at 180iterations finished qdiffx linear iterations at : 14:12:57 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 3.2791839E-04 7.8792572E-03 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 14:13:00 12.005u 0.154s 0:41.60 29.2% 0+0k 0+0io 0pf+0w