Sun Oct 9 16:39:39 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 Sun Oct 9 2011 at 16:39:39 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: GLM 45 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.6366465 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): 8.999001 64.91700 ymin,ymax (A): -17.45400 30.50200 zmin,zma (A): -30.18200 23.18600 x,y,z range (A): 55.91800 47.95600 53.36800 scale (grids/A): 0.6366465 object centre (A): 36.95800 6.524000 -3.498000 number of atom coordinates read : 2463 total number of charged atoms : 2359 net assigned charge : 0.4060059 assigned positive charge : 365.0229 centred at (gu) : 91.60732 90.23146 92.33018 assigned negative charge : -364.6180 centred at (gu) : 91.45630 90.18456 92.19035 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6880 nv = 96 ne = 84 npr = 48791 no. pairs analyzed = 48791 no. exposed pairs = 3249 no. arc points = 23476 no. surface atoms = 1098 nbur = 1365 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3581 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3600000 number of dielectric boundary points 3634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2255 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8185 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5545340E-09 2.2758796E-08 midg,1,midg; midg,igrid,midg -4.5300244E-09 4.7739519E-09 1,midg,midg; igrid,midg,midg -1.0797462E-08 2.0886482E-08 gauss-seidel spectral radius is 0.9872175 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 16:39:39 rms-change max change #iterations 0.1382673 25.69834 at 10iterations 1.3616594E-02 2.098785 at 20iterations 1.3616992E-03 0.2135830 at 30iterations 1.6775208E-04 2.4881363E-02 at 40iterations 3.4973600E-05 5.0134659E-03 at 50iterations finished qdiffx linear iterations at : 16:39:42 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.4973600E-05 5.0134659E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 16:39:43 3.440u 0.168s 0:03.89 92.5% 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 Sun Oct 9 2011 at 16:39:43 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: GLM 45 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.909940 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): 8.999001 64.91700 ymin,ymax (A): -17.45400 30.50200 zmin,zma (A): -30.18200 23.18600 x,y,z range (A): 55.91800 47.95600 53.36800 scale (grids/A): 1.909940 object centre (A): 36.95800 6.524000 -3.498000 number of atom coordinates read : 2463 total number of charged atoms : 2359 net assigned charge : 0.4060059 assigned positive charge : 365.0229 centred at (gu) : 94.82137 90.69365 96.99022 assigned negative charge : -364.6180 centred at (gu) : 94.36879 90.55366 96.57104 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 73554 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23476 grid for indexing accessible points = 1.400000 m= 26214 mr = 49119 m= 4250 mr = 18897 m= 294 mr = 2525 m= 3 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 0.6300000 number of dielectric boundary points 33656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 18565 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) : 0.6366465 object centre at (A) : 36.95800 6.524000 -3.498000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7869864E-02 -2.3162032E-03 midg,1,midg; midg,igrid,midg -6.6604954E-03 7.6215039E-03 1,midg,midg; igrid,midg,midg -1.3537966E-02 1.9869160E-02 gauss-seidel spectral radius is 0.9986429 estimated iterations to convergence 215 setup time was (sec) 0.9500000 now iterating at: 16:39:44 rms-change max change #iterations 4.135055 170.7827 at 10iterations 1.950934 60.21803 at 20iterations 0.9143578 31.67312 at 30iterations 0.4305334 14.92320 at 40iterations 0.2031607 6.682550 at 50iterations 9.5615648E-02 3.317948 at 60iterations 4.4955533E-02 1.622423 at 70iterations 2.1045545E-02 0.7380522 at 80iterations 9.9365897E-03 0.3101196 at 90iterations 4.6710162E-03 0.1559792 at 100iterations 2.2002114E-03 6.6951752E-02 at 110iterations 1.0383021E-03 3.2869339E-02 at 120iterations finished qdiffx linear iterations at : 16:39:51 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 1.0383021E-03 3.2869339E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 16:39:51 8.244u 0.201s 0:08.75 96.4% 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 Sun Oct 9 2011 at 16:39:51 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 !!! WARNING: GLM 45 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.864909 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): 8.999001 64.91700 ymin,ymax (A): -17.45400 30.50200 zmin,zma (A): -30.18200 23.18600 x,y,z range (A): 55.91800 47.95600 53.36800 scale (grids/A): 2.864909 object centre (A): 36.95800 6.524000 -3.498000 number of atom coordinates read : 2463 total number of charged atoms : 2359 net assigned charge : 0.4060059 assigned positive charge : 365.0229 centred at (gu) : 97.23199 91.04034 100.4852 assigned negative charge : -364.6180 centred at (gu) : 96.55311 90.83039 99.85652 start vw surface at 0.2500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 170281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23476 grid for indexing accessible points = 1.400000 m= 83950 mr = 119783 m= 30864 mr = 67398 m= 7611 mr = 24525 m= 1209 mr = 5628 m= 114 mr = 770 m= 0 mr = 52 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 3630 time to turn everything in is 1.510000 number of dielectric boundary points 75873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 18867 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) : 1.909940 object centre at (A) : 36.95800 6.524000 -3.498000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1387803 -8.9096203E-02 midg,1,midg; midg,igrid,midg -7.5283296E-02 8.3664827E-02 1,midg,midg; igrid,midg,midg -0.1126021 7.8878045E-02 gauss-seidel spectral radius is 0.9992723 estimated iterations to convergence 293 setup time was (sec) 1.800000 now iterating at: 16:39:53 rms-change max change #iterations 9.756768 451.2871 at 10iterations 5.767720 155.4491 at 20iterations 3.385247 74.16228 at 30iterations 1.981036 50.73824 at 40iterations 1.155802 21.95652 at 50iterations 0.6715395 12.49320 at 60iterations 0.3903179 8.976267 at 70iterations 0.2263195 4.359173 at 80iterations 0.1311213 2.334949 at 90iterations 7.5962901E-02 1.457881 at 100iterations 4.3986686E-02 0.8083968 at 110iterations 2.5454676E-02 0.5101051 at 120iterations 1.4696466E-02 0.2607665 at 130iterations 8.4932260E-03 0.1546006 at 140iterations 4.9157459E-03 8.9088440E-02 at 150iterations 2.8384575E-03 5.0150871E-02 at 160iterations 1.6442408E-03 3.1484604E-02 at 170iterations 9.5214136E-04 1.8301249E-02 at 180iterations finished qdiffx linear iterations at : 16:40:04 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 9.5214136E-04 1.8301249E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 16:40:04 12.313u 0.204s 0:12.81 97.6% 0+0k 0+0io 0pf+0w