Sun Oct 9 22:05:28 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 22:05:28 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 163 has a net charge of -0.6000 !!! WARNING: ZN6 634 has a net charge of 1.4000 !!! WARNING: ZN6 635 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6336662 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): 17.22000 73.40100 ymin,ymax (A): -14.33500 37.59000 zmin,zma (A): -2.169000 49.50300 x,y,z range (A): 56.18100 51.92500 51.67200 scale (grids/A): 0.6336662 object centre (A): 45.31050 11.62750 23.66700 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 7.825011 assigned positive charge : 392.8179 centred at (gu) : 90.90013 90.96899 90.22347 assigned negative charge : -384.9936 centred at (gu) : 90.94466 90.88686 90.26032 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6648 nv = 96 ne = 84 npr = 52148 no. pairs analyzed = 52148 no. exposed pairs = 3172 no. arc points = 22435 no. surface atoms = 1064 nbur = 1500 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3561 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2800000 number of dielectric boundary points 3406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2194 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8242 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2399064E-08 6.1131757E-09 midg,1,midg; midg,igrid,midg 1.2123097E-09 2.1354642E-08 1,midg,midg; igrid,midg,midg 1.1361305E-08 6.0921956E-09 gauss-seidel spectral radius is 0.9870926 estimated iterations to convergence 72 setup time was (sec) 0.4900000 now iterating at: 22:05:29 rms-change max change #iterations 0.1445021 27.28841 at 10iterations 1.3860507E-02 2.399567 at 20iterations 1.3332460E-03 0.2122173 at 30iterations 1.2910717E-04 1.7805576E-02 at 40iterations 1.2627183E-05 1.8038750E-03 at 50iterations finished qdiffx linear iterations at : 22:05:32 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 1.2627183E-05 1.8038750E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 22:05:32 3.262u 0.231s 0:03.84 90.8% 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 Sun Oct 9 2011 at 22:05:32 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 163 has a net charge of -0.6000 !!! WARNING: ZN6 634 has a net charge of 1.4000 !!! WARNING: ZN6 635 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.900999 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): 17.22000 73.40100 ymin,ymax (A): -14.33500 37.59000 zmin,zma (A): -2.169000 49.50300 x,y,z range (A): 56.18100 51.92500 51.67200 scale (grids/A): 1.900999 object centre (A): 45.31050 11.62750 23.66700 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 7.825011 assigned positive charge : 392.8179 centred at (gu) : 92.70007 92.90596 90.66943 assigned negative charge : -384.9936 centred at (gu) : 92.83373 92.66028 90.78078 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22435 grid for indexing accessible points = 1.400000 m= 24091 mr = 49420 m= 3603 mr = 17312 m= 219 mr = 2093 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 970 time to turn everything in is 0.5200000 number of dielectric boundary points 31498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19096 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) : 0.6336662 object centre at (A) : 45.31050 11.62750 23.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0508634E-02 -9.6205426E-03 midg,1,midg; midg,igrid,midg 1.2828296E-03 4.3920528E-02 1,midg,midg; igrid,midg,midg -3.7583793E-03 2.8217843E-02 gauss-seidel spectral radius is 0.9986199 estimated iterations to convergence 213 setup time was (sec) 0.7900000 now iterating at: 22:05:33 rms-change max change #iterations 4.226823 171.2408 at 10iterations 1.961567 77.21081 at 20iterations 0.9161955 29.05407 at 30iterations 0.4259613 13.14345 at 40iterations 0.1982228 6.206886 at 50iterations 9.2607267E-02 3.025172 at 60iterations 4.3062706E-02 1.519688 at 70iterations 2.0125484E-02 0.6261578 at 80iterations 9.3927700E-03 0.3003807 at 90iterations 4.3760785E-03 0.1452637 at 100iterations 2.0407964E-03 6.4273834E-02 at 110iterations 9.5150626E-04 3.0228615E-02 at 120iterations finished qdiffx linear iterations at : 22:05:40 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 9.5150626E-04 3.0228615E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 22:05:40 7.413u 0.255s 0:07.96 96.2% 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 Sun Oct 9 2011 at 22:05:40 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 163 has a net charge of -0.6000 !!! WARNING: ZN6 634 has a net charge of 1.4000 !!! WARNING: ZN6 635 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.851498 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): 17.22000 73.40100 ymin,ymax (A): -14.33500 37.59000 zmin,zma (A): -2.169000 49.50300 x,y,z range (A): 56.18100 51.92500 51.67200 scale (grids/A): 2.851498 object centre (A): 45.31050 11.62750 23.66700 number of atom coordinates read : 2564 total number of charged atoms : 2432 net assigned charge : 7.825011 assigned positive charge : 392.8179 centred at (gu) : 94.04975 94.35889 91.00417 assigned negative charge : -384.9936 centred at (gu) : 94.25062 93.99046 91.17117 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 167797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22435 grid for indexing accessible points = 1.400000 m= 80313 mr = 120279 m= 27087 mr = 64881 m= 6187 mr = 20995 m= 894 mr = 4445 m= 72 mr = 617 m= 0 mr = 46 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 3205 time to turn everything in is 1.290000 number of dielectric boundary points 71087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 19454 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) : 1.900999 object centre at (A) : 45.31050 11.62750 23.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2584243 -0.2540943 midg,1,midg; midg,igrid,midg -0.1928279 0.5609328 1,midg,midg; igrid,midg,midg 1.0978798E-02 0.2480984 gauss-seidel spectral radius is 0.9992554 estimated iterations to convergence 289 setup time was (sec) 1.590000 now iterating at: 22:05:42 rms-change max change #iterations 9.944899 372.4748 at 10iterations 5.813416 128.2487 at 20iterations 3.361984 67.35741 at 30iterations 1.941270 41.68099 at 40iterations 1.118326 21.72491 at 50iterations 0.6441339 12.90932 at 60iterations 0.3704022 6.530327 at 70iterations 0.2127062 4.071837 at 80iterations 0.1219604 2.310847 at 90iterations 7.0177607E-02 1.335056 at 100iterations 4.0226761E-02 0.7794647 at 110iterations 2.3078162E-02 0.4382057 at 120iterations 1.3227151E-02 0.2404413 at 130iterations 7.5891404E-03 0.1381474 at 140iterations 4.3395869E-03 7.5561523E-02 at 150iterations 2.4936225E-03 4.3643713E-02 at 160iterations 1.4290094E-03 2.5668144E-02 at 170iterations 8.2199299E-04 1.8079758E-02 at 180iterations finished qdiffx linear iterations at : 22:05:52 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 8.2199299E-04 1.8079758E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 22:05:53 12.040u 0.251s 0:12.69 96.8% 0+0k 0+0io 0pf+0w