Tue Oct 11 03:40:42 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 Tue Oct 11 2011 at 03:40:42 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: 351 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6706478 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): -9.342999 36.59300 ymin,ymax (A): -26.78100 21.27800 zmin,zma (A): -7.845000 45.23800 x,y,z range (A): 45.93600 48.05900 53.08300 scale (grids/A): 0.6706478 object centre (A): 13.62500 -2.751500 18.69650 number of atom coordinates read : 2869 total number of charged atoms : 2701 net assigned charge : 0.7010238 assigned positive charge : 433.5738 centred at (gu) : 89.54966 90.64194 91.25009 assigned negative charge : -432.8732 centred at (gu) : 89.22144 90.53984 91.26366 start vw surface at 0.1200000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8498 nv = 96 ne = 84 npr = 59848 no. pairs analyzed = 59848 no. exposed pairs = 3271 no. arc points = 22689 no. surface atoms = 1115 nbur = 1754 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 521 mr = 5015 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 64 time to turn everything in is 0.3400000 number of dielectric boundary points 3940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2210 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2512936E-09 -1.3990546E-09 midg,1,midg; midg,igrid,midg -2.3466773E-08 3.6562771E-08 1,midg,midg; igrid,midg,midg -1.0444032E-07 8.5797666E-08 gauss-seidel spectral radius is 0.9884908 estimated iterations to convergence 76 setup time was (sec) 0.6400000 now iterating at: 03:40:43 rms-change max change #iterations 0.1981474 28.05379 at 10iterations 2.2573294E-02 3.129395 at 20iterations 2.6846644E-03 0.3940468 at 30iterations 4.2401734E-04 4.8353434E-02 at 40iterations 1.1708307E-04 1.5146255E-02 at 50iterations finished qdiffx linear iterations at : 03:40:47 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 1.1708307E-04 1.5146255E-02 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 03:40:48 4.528u 0.384s 0:05.76 85.0% 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 Oct 11 2011 at 03:40:48 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: 351 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.011943 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): -9.342999 36.59300 ymin,ymax (A): -26.78100 21.27800 zmin,zma (A): -7.845000 45.23800 x,y,z range (A): 45.93600 48.05900 53.08300 scale (grids/A): 2.011943 object centre (A): 13.62500 -2.751500 18.69650 number of atom coordinates read : 2869 total number of charged atoms : 2701 net assigned charge : 0.7010238 assigned positive charge : 433.5738 centred at (gu) : 88.64863 91.92571 93.74985 assigned negative charge : -432.8732 centred at (gu) : 87.66402 91.61933 93.79051 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 90850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22689 grid for indexing accessible points = 1.400000 m= 36660 mr = 65439 m= 6510 mr = 28296 m= 454 mr = 4296 m= 11 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 3067 time to turn everything in is 0.7400000 number of dielectric boundary points 36264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 21390 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) : 0.6706478 object centre at (A) : 13.62500 -2.751500 18.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4469525E-03 1.0285196E-02 midg,1,midg; midg,igrid,midg -1.2532292E-02 9.2385765E-03 1,midg,midg; igrid,midg,midg -3.7712947E-02 7.0809312E-02 gauss-seidel spectral radius is 0.9987877 estimated iterations to convergence 227 setup time was (sec) 1.050000 now iterating at: 03:40:49 rms-change max change #iterations 5.017436 200.1207 at 10iterations 2.470214 90.22195 at 20iterations 1.211964 35.00401 at 30iterations 0.5952010 16.80240 at 40iterations 0.2923838 8.505003 at 50iterations 0.1433554 4.384239 at 60iterations 7.0393108E-02 2.090487 at 70iterations 3.4587324E-02 0.9435577 at 80iterations 1.6972791E-02 0.4711289 at 90iterations 8.3110807E-03 0.2326851 at 100iterations 4.0952940E-03 0.1120901 at 110iterations 2.0240436E-03 6.4029694E-02 at 120iterations finished qdiffx linear iterations at : 03:40:59 total time elapsed so far: 11.07000 # loops : 120 mean,max change (kT/e) : 2.0240436E-03 6.4029694E-02 energy calculations done at 11.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.23000 DelPhi exited at 03:41:00 11.234u 0.423s 0:12.12 96.1% 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 Oct 11 2011 at 03:41:00 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: 351 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.017915 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): -9.342999 36.59300 ymin,ymax (A): -26.78100 21.27800 zmin,zma (A): -7.845000 45.23800 x,y,z range (A): 45.93600 48.05900 53.08300 scale (grids/A): 3.017915 object centre (A): 13.62500 -2.751500 18.69650 number of atom coordinates read : 2869 total number of charged atoms : 2701 net assigned charge : 0.7010238 assigned positive charge : 433.5738 centred at (gu) : 87.97292 92.88824 95.62476 assigned negative charge : -432.8732 centred at (gu) : 86.49591 92.42899 95.68578 start vw surface at 0.1300000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 209536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22689 grid for indexing accessible points = 1.400000 m= 114314 mr = 157132 m= 46330 mr = 95988 m= 12127 mr = 38743 m= 1880 mr = 9367 m= 162 mr = 1300 m= 3 mr = 82 m= 0 mr = 2 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 9931 time to turn everything in is 2.010000 number of dielectric boundary points 81738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 21607 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) : 2.011943 object centre at (A) : 13.62500 -2.751500 18.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7991019E-02 0.3540539 midg,1,midg; midg,igrid,midg -0.1335887 4.8818197E-02 1,midg,midg; igrid,midg,midg -0.2031605 0.5865270 gauss-seidel spectral radius is 0.9992952 estimated iterations to convergence 297 setup time was (sec) 2.350000 now iterating at: 03:41:03 rms-change max change #iterations 11.47206 425.3760 at 10iterations 6.791206 140.6090 at 20iterations 4.015596 74.94207 at 30iterations 2.365726 42.88250 at 40iterations 1.391869 23.53056 at 50iterations 0.8172342 14.30171 at 60iterations 0.4797420 8.022594 at 70iterations 0.2808257 4.550395 at 80iterations 0.1644500 2.590256 at 90iterations 9.6150488E-02 1.589836 at 100iterations 5.6306235E-02 0.9207449 at 110iterations 3.2872979E-02 0.5301046 at 120iterations 1.9272445E-02 0.3401127 at 130iterations 1.1295069E-02 0.1950989 at 140iterations 6.6089383E-03 0.1073074 at 150iterations 3.8756083E-03 6.4178467E-02 at 160iterations 2.2861073E-03 3.6678314E-02 at 170iterations 1.3575297E-03 2.2149801E-02 at 180iterations finished qdiffx linear iterations at : 03:41:19 total time elapsed so far: 18.65000 # loops : 180 mean,max change (kT/e) : 1.3575297E-03 2.2149801E-02 energy calculations done at 18.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.81000 DelPhi exited at 03:41:20 18.812u 0.462s 0:19.93 96.6% 0+0k 0+0io 0pf+0w