Tue Nov 22 14:13:00 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+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 Tue Nov 22 2011 at 14:13:08 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 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: 0.5955667 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): -24.53100 35.24400 ymin,ymax (A): -19.16700 20.74400 zmin,zma (A): -2.836000 39.86600 x,y,z range (A): 59.77500 39.91100 42.70200 scale (grids/A): 0.5955667 object centre (A): 5.356502 0.7884998 18.51500 number of atom coordinates read : 2171 total number of charged atoms : 1865 net assigned charge : 4.000007 assigned positive charge : 294.8130 centred at (gu) : 89.71429 90.47047 90.11208 assigned negative charge : -290.8133 centred at (gu) : 89.74993 90.55979 90.23454 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4853 nv = 96 ne = 84 npr = 40277 no. pairs analyzed = 40277 no. exposed pairs = 2437 no. arc points = 17233 no. surface atoms = 829 nbur = 1342 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 226 mr = 2688 m= 1 mr = 19 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 0.2200000 number of dielectric boundary points 2373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5849 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2622874E-09 -1.5019774E-09 midg,1,midg; midg,igrid,midg 3.2373515E-09 -7.3728290E-10 1,midg,midg; igrid,midg,midg 2.4987750E-09 6.0834632E-10 gauss-seidel spectral radius is 0.9853619 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 14:13:11 rms-change max change #iterations 8.7575711E-02 16.80983 at 10iterations 7.2874674E-03 1.515303 at 20iterations 5.8902527E-04 9.5062256E-02 at 30iterations 4.9991679E-05 1.0166168E-02 at 40iterations 4.2853103E-06 8.5067749E-04 at 50iterations finished qdiffx linear iterations at : 14:13:19 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 4.2853103E-06 8.5067749E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 14:13:21 3.153u 0.169s 0:13.64 24.2% 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 Nov 22 2011 at 14:13:23 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 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: 1.786700 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): -24.53100 35.24400 ymin,ymax (A): -19.16700 20.74400 zmin,zma (A): -2.836000 39.86600 x,y,z range (A): 59.77500 39.91100 42.70200 scale (grids/A): 1.786700 object centre (A): 5.356502 0.7884998 18.51500 number of atom coordinates read : 2171 total number of charged atoms : 1865 net assigned charge : 4.000007 assigned positive charge : 294.8130 centred at (gu) : 89.14258 91.41136 90.33657 assigned negative charge : -290.8133 centred at (gu) : 89.24992 91.67949 90.70372 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 19008 mr = 36218 m= 2422 mr = 14389 m= 92 mr = 1400 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 440 time to turn everything in is 0.3600000 number of dielectric boundary points 21791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14516 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) : 0.5955667 object centre at (A) : 5.356502 0.7884998 18.51500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7509697E-03 -3.7645744E-03 midg,1,midg; midg,igrid,midg 4.4866488E-03 -3.9993451E-04 1,midg,midg; igrid,midg,midg 3.0673677E-02 1.9714791E-02 gauss-seidel spectral radius is 0.9983791 estimated iterations to convergence 197 setup time was (sec) 0.6300000 now iterating at: 14:13:29 rms-change max change #iterations 3.162750 145.5932 at 10iterations 1.382840 54.45065 at 20iterations 0.6043143 25.47135 at 30iterations 0.2641698 10.68363 at 40iterations 0.1154928 4.882568 at 50iterations 5.0262090E-02 1.837619 at 60iterations 2.2068614E-02 0.8976574 at 70iterations 9.6384771E-03 0.3710322 at 80iterations 4.2139902E-03 0.1453314 at 90iterations 1.8506442E-03 7.1843624E-02 at 100iterations 8.0682908E-04 3.0826569E-02 at 110iterations 3.5358971E-04 1.3227463E-02 at 120iterations finished qdiffx linear iterations at : 14:13:49 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 3.5358971E-04 1.3227463E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 14:13:57 7.017u 0.158s 0:33.87 21.1% 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 14:13:58 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 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: 2.680050 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): -24.53100 35.24400 ymin,ymax (A): -19.16700 20.74400 zmin,zma (A): -2.836000 39.86600 x,y,z range (A): 59.77500 39.91100 42.70200 scale (grids/A): 2.680050 object centre (A): 5.356502 0.7884998 18.51500 number of atom coordinates read : 2171 total number of charged atoms : 1865 net assigned charge : 4.000007 assigned positive charge : 294.8130 centred at (gu) : 88.71383 92.11709 90.50475 assigned negative charge : -290.8133 centred at (gu) : 88.87493 92.51922 91.05569 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 120700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 62475 mr = 87312 m= 21567 mr = 52135 m= 4079 mr = 17480 m= 400 mr = 2953 m= 13 mr = 250 m= 0 mr = 2 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1484 time to turn everything in is 0.9100000 number of dielectric boundary points 49102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 14917 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) : 1.786700 object centre at (A) : 5.356502 0.7884998 18.51500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6244037E-02 -4.4949405E-02 midg,1,midg; midg,igrid,midg 3.5970550E-02 2.4671126E-03 1,midg,midg; igrid,midg,midg 0.3600487 0.2087588 gauss-seidel spectral radius is 0.9991688 estimated iterations to convergence 274 setup time was (sec) 1.210000 now iterating at: 14:14:05 rms-change max change #iterations 7.623611 298.3416 at 10iterations 4.263579 105.5770 at 20iterations 2.380972 53.46589 at 30iterations 1.323538 29.01306 at 40iterations 0.7360254 16.16633 at 50iterations 0.4072478 9.150217 at 60iterations 0.2262709 4.368988 at 70iterations 0.1253334 2.667305 at 80iterations 6.9363549E-02 1.462732 at 90iterations 3.8467564E-02 0.8278303 at 100iterations 2.1324662E-02 0.4629469 at 110iterations 1.1834024E-02 0.2632093 at 120iterations 6.5671536E-03 0.1401968 at 130iterations 3.6402580E-03 7.9855919E-02 at 140iterations 2.0160624E-03 4.3593407E-02 at 150iterations 1.1191114E-03 2.6066780E-02 at 160iterations 6.1914662E-04 1.6078711E-02 at 170iterations 3.4281256E-04 7.4253082E-03 at 180iterations finished qdiffx linear iterations at : 14:14:35 total time elapsed so far: 11.08000 # loops : 180 mean,max change (kT/e) : 3.4281256E-04 7.4253082E-03 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 14:14:37 11.253u 0.215s 0:39.40 29.0% 0+0k 0+0io 0pf+0w