Sat Oct 8 11:36:23 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+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 Sat Oct 8 2011 at 11:36:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6245066 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): 35.22300 92.22800 ymin,ymax (A): 33.85500 84.43500 zmin,zma (A): 20.75400 69.76800 x,y,z range (A): 57.00500 50.58000 49.01400 scale (grids/A): 0.6245066 object centre (A): 63.72550 59.14500 45.26100 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -5.499964 assigned positive charge : 510.4684 centred at (gu) : 90.21904 89.97614 89.29900 assigned negative charge : -515.9693 centred at (gu) : 90.13995 90.14445 89.29759 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8222 nv = 96 ne = 84 npr = 72358 no. pairs analyzed = 72358 no. exposed pairs = 3721 no. arc points = 25168 no. surface atoms = 1268 nbur = 2088 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 4839 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.3900000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2525 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0608230E-09 -4.2625632E-09 midg,1,midg; midg,igrid,midg 1.1607844E-08 -2.2224533E-08 1,midg,midg; igrid,midg,midg -1.2498258E-08 2.9637046E-09 gauss-seidel spectral radius is 0.9867689 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 11:36:24 rms-change max change #iterations 0.1555784 19.61704 at 10iterations 1.4523427E-02 2.129303 at 20iterations 1.3421113E-03 0.1638727 at 30iterations 1.2952273E-04 1.6986847E-02 at 40iterations 1.2208777E-05 1.4686584E-03 at 50iterations finished qdiffx linear iterations at : 11:36:27 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.2208777E-05 1.4686584E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 11:36:27 3.557u 0.145s 0:04.02 91.7% 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 11:36:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.873520 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): 35.22300 92.22800 ymin,ymax (A): 33.85500 84.43500 zmin,zma (A): 20.75400 69.76800 x,y,z range (A): 57.00500 50.58000 49.01400 scale (grids/A): 1.873520 object centre (A): 63.72550 59.14500 45.26100 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -5.499964 assigned positive charge : 510.4684 centred at (gu) : 90.65616 89.92740 87.89589 assigned negative charge : -515.9693 centred at (gu) : 90.41932 90.43282 87.89207 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 90013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25168 grid for indexing accessible points = 1.400000 m= 32862 mr = 65162 m= 5110 mr = 25334 m= 284 mr = 3352 m= 6 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2877 time to turn everything in is 0.6500000 number of dielectric boundary points 34329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 25166 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) : 0.6245066 object centre at (A) : 63.72550 59.14500 45.26100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4275860E-02 -2.0516643E-02 midg,1,midg; midg,igrid,midg 3.9720759E-03 -4.2318538E-02 1,midg,midg; igrid,midg,midg -2.0359728E-02 1.4041860E-02 gauss-seidel spectral radius is 0.9986440 estimated iterations to convergence 215 setup time was (sec) 0.9600000 now iterating at: 11:36:28 rms-change max change #iterations 4.789134 195.3365 at 10iterations 2.241588 67.65424 at 20iterations 1.057847 32.49740 at 30iterations 0.4957364 13.93407 at 40iterations 0.2333363 7.740441 at 50iterations 0.1099347 3.292959 at 60iterations 5.1660739E-02 1.421081 at 70iterations 2.4343712E-02 0.6887512 at 80iterations 1.1428509E-02 0.3717003 at 90iterations 5.3918255E-03 0.1661758 at 100iterations 2.5267815E-03 6.9602966E-02 at 110iterations 1.1959958E-03 3.5531938E-02 at 120iterations finished qdiffx linear iterations at : 11:36:35 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.1959958E-03 3.5531938E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 11:36:36 7.744u 0.197s 0:08.48 93.5% 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 11:36:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.810280 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): 35.22300 92.22800 ymin,ymax (A): 33.85500 84.43500 zmin,zma (A): 20.75400 69.76800 x,y,z range (A): 57.00500 50.58000 49.01400 scale (grids/A): 2.810280 object centre (A): 63.72550 59.14500 45.26100 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -5.499964 assigned positive charge : 510.4684 centred at (gu) : 90.98420 89.89088 86.84352 assigned negative charge : -515.9693 centred at (gu) : 90.62872 90.64899 86.83820 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 208218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25168 grid for indexing accessible points = 1.400000 m= 107093 mr = 156991 m= 39225 mr = 89781 m= 9168 mr = 32809 m= 1253 mr = 7110 m= 70 mr = 795 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 9685 time to turn everything in is 1.670000 number of dielectric boundary points 77511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 25632 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) : 1.873520 object centre at (A) : 63.72550 59.14500 45.26100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3211937 -0.2905200 midg,1,midg; midg,igrid,midg -4.0015146E-02 -0.4756095 1,midg,midg; igrid,midg,midg 0.2180385 0.1738556 gauss-seidel spectral radius is 0.9992621 estimated iterations to convergence 291 setup time was (sec) 2.000000 now iterating at: 11:36:38 rms-change max change #iterations 11.18339 309.1813 at 10iterations 6.525597 135.0634 at 20iterations 3.774405 65.46533 at 30iterations 2.186750 35.83758 at 40iterations 1.262638 19.35172 at 50iterations 0.7273861 12.03414 at 60iterations 0.4196279 7.280866 at 70iterations 0.2416273 4.155304 at 80iterations 0.1392915 2.286953 at 90iterations 8.0114476E-02 1.326359 at 100iterations 4.6021197E-02 0.7880292 at 110iterations 2.6550574E-02 0.4417388 at 120iterations 1.5217885E-02 0.2364273 at 130iterations 8.7646702E-03 0.1441410 at 140iterations 5.0470037E-03 8.6037159E-02 at 150iterations 2.9007727E-03 4.7140121E-02 at 160iterations 1.6688218E-03 2.8751373E-02 at 170iterations 9.5975772E-04 1.5284538E-02 at 180iterations finished qdiffx linear iterations at : 11:36:48 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 9.5975772E-04 1.5284538E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 11:36:49 12.744u 0.194s 0:13.28 97.3% 0+0k 0+0io 0pf+0w