Sat Oct 8 18:53:45 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 18:53:45 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 583 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7106497 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): -28.65600 17.58800 ymin,ymax (A): -23.97000 23.27500 zmin,zma (A): -12.15100 37.94400 x,y,z range (A): 46.24400 47.24500 50.09500 scale (grids/A): 0.7106497 object centre (A): -5.534000 -0.3474998 12.89650 number of atom coordinates read : 2061 total number of charged atoms : 1924 net assigned charge : 4.500007 assigned positive charge : 304.6940 centred at (gu) : 89.36841 88.67976 90.04115 assigned negative charge : -300.1943 centred at (gu) : 89.27084 88.85020 89.84608 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7155 nv = 96 ne = 84 npr = 43294 no. pairs analyzed = 43294 no. exposed pairs = 2466 no. arc points = 17438 no. surface atoms = 822 nbur = 1239 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 508 mr = 4138 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2600000 number of dielectric boundary points 3439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1525 ## 123 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7878 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0848770E-08 1.3882382E-07 midg,1,midg; midg,igrid,midg 1.6282038E-07 -3.6744730E-08 1,midg,midg; igrid,midg,midg -1.1882180E-08 7.9154688E-08 gauss-seidel spectral radius is 0.9896808 estimated iterations to convergence 80 setup time was (sec) 0.5800000 now iterating at: 18:53:46 rms-change max change #iterations 0.2100562 28.63429 at 10iterations 2.6010010E-02 4.307154 at 20iterations 3.2501139E-03 0.5144653 at 30iterations 4.0189005E-04 5.9448242E-02 at 40iterations 4.9986767E-05 7.1029663E-03 at 50iterations finished qdiffx linear iterations at : 18:53:50 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 4.9986767E-05 7.1029663E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 18:53:50 4.416u 0.410s 0:05.08 94.8% 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 18:53:50 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 583 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.131949 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): -28.65600 17.58800 ymin,ymax (A): -23.97000 23.27500 zmin,zma (A): -12.15100 37.94400 x,y,z range (A): 46.24400 47.24500 50.09500 scale (grids/A): 2.131949 object centre (A): -5.534000 -0.3474998 12.89650 number of atom coordinates read : 2061 total number of charged atoms : 1924 net assigned charge : 4.500007 assigned positive charge : 304.6940 centred at (gu) : 88.10537 86.03921 90.12334 assigned negative charge : -300.1943 centred at (gu) : 87.81268 86.55083 89.53845 start vw surface at 0.1000000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17438 grid for indexing accessible points = 1.400000 m= 29668 mr = 53666 m= 5897 mr = 22558 m= 605 mr = 3971 m= 18 mr = 262 m= 0 mr = 5 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1344 time to turn everything in is 0.6200000 number of dielectric boundary points 31664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15308 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) : 0.7106497 object centre at (A) : -5.534000 -0.3474998 12.89650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3786163E-02 1.9726686E-02 midg,1,midg; midg,igrid,midg 3.0331191E-02 2.4992325E-03 1,midg,midg; igrid,midg,midg 1.6611492E-02 7.6262183E-02 gauss-seidel spectral radius is 0.9988442 estimated iterations to convergence 233 setup time was (sec) 0.9700000 now iterating at: 18:53:52 rms-change max change #iterations 4.651068 220.7189 at 10iterations 2.311154 80.64606 at 20iterations 1.155985 35.07255 at 30iterations 0.5788144 17.97468 at 40iterations 0.2881265 8.991793 at 50iterations 0.1438895 4.249451 at 60iterations 7.1969666E-02 2.285510 at 70iterations 3.5714414E-02 1.101936 at 80iterations 1.7808499E-02 0.4984283 at 90iterations 8.8746389E-03 0.2710533 at 100iterations 4.4141617E-03 0.1275826 at 110iterations 2.2065972E-03 6.0989380E-02 at 120iterations finished qdiffx linear iterations at : 18:54:01 total time elapsed so far: 10.46000 # loops : 120 mean,max change (kT/e) : 2.2065972E-03 6.0989380E-02 energy calculations done at 10.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.62000 DelPhi exited at 18:54:02 10.628u 0.458s 0:11.35 97.5% 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 18:54:02 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 583 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.197924 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): -28.65600 17.58800 ymin,ymax (A): -23.97000 23.27500 zmin,zma (A): -12.15100 37.94400 x,y,z range (A): 46.24400 47.24500 50.09500 scale (grids/A): 3.197924 object centre (A): -5.534000 -0.3474998 12.89650 number of atom coordinates read : 2061 total number of charged atoms : 1924 net assigned charge : 4.500007 assigned positive charge : 304.6940 centred at (gu) : 87.15810 84.05888 90.18506 assigned negative charge : -300.1943 centred at (gu) : 86.71896 84.82629 89.30774 start vw surface at 0.1100000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 175270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17438 grid for indexing accessible points = 1.400000 m= 92445 mr = 128979 m= 37629 mr = 77333 m= 11316 mr = 31110 m= 2344 mr = 8670 m= 284 mr = 1650 m= 13 mr = 150 m= 0 mr = 2 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 4430 time to turn everything in is 1.950000 number of dielectric boundary points 71407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 15392 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) : 2.131949 object centre at (A) : -5.534000 -0.3474998 12.89650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1456216 0.1799212 midg,1,midg; midg,igrid,midg 0.2136474 2.9011868E-02 1,midg,midg; igrid,midg,midg 2.1285361E-02 0.7414529 gauss-seidel spectral radius is 0.9993047 estimated iterations to convergence 299 setup time was (sec) 2.280000 now iterating at: 18:54:05 rms-change max change #iterations 10.14582 376.1217 at 10iterations 5.947148 123.2701 at 20iterations 3.482786 66.14896 at 30iterations 2.036093 40.66890 at 40iterations 1.193361 20.49995 at 50iterations 0.6955831 11.74321 at 60iterations 0.4073840 7.041321 at 70iterations 0.2385861 4.238564 at 80iterations 0.1391314 2.344994 at 90iterations 8.1132270E-02 1.536453 at 100iterations 4.7517780E-02 0.8213301 at 110iterations 2.7696621E-02 0.4687452 at 120iterations 1.6149841E-02 0.2671017 at 130iterations 9.4784014E-03 0.1633987 at 140iterations 5.5367230E-03 9.9436760E-02 at 150iterations 3.2440480E-03 5.5189133E-02 at 160iterations 1.8958279E-03 3.0073762E-02 at 170iterations 1.1087110E-03 1.8441916E-02 at 180iterations finished qdiffx linear iterations at : 18:54:20 total time elapsed so far: 18.23000 # loops : 180 mean,max change (kT/e) : 1.1087110E-03 1.8441916E-02 energy calculations done at 18.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.40000 DelPhi exited at 18:54:21 18.401u 0.460s 0:19.14 98.5% 0+0k 0+0io 0pf+0w