Sun Oct 9 08:26:41 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 08:26:41 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5868 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4820060 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 0.4820060 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.985961 assigned positive charge : 881.0883 centred at (gu) : 90.21787 89.74046 89.17110 assigned negative charge : -886.0815 centred at (gu) : 90.33809 89.72434 89.13749 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8507 nv = 96 ne = 84 npr = 117632 no. pairs analyzed = 117632 no. exposed pairs = 7387 no. arc points = 51578 no. surface atoms = 2475 nbur = 3393 mkacc time = 0.2500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 289 mr = 4320 m= 0 mr = 1 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4854 ## 840 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 11635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9850944E-11 9.1953875E-12 midg,1,midg; midg,igrid,midg -3.4329754E-11 -3.3377658E-12 1,midg,midg; igrid,midg,midg 8.1297719E-11 -1.3343619E-10 gauss-seidel spectral radius is 0.9780820 estimated iterations to convergence 56 setup time was (sec) 0.7800000 now iterating at: 08:26:42 rms-change max change #iterations 5.5670686E-02 8.149422 at 10iterations 3.2614002E-03 0.6959305 at 20iterations 5.2103633E-04 0.1298981 at 30iterations 1.4454940E-04 3.4736633E-02 at 40iterations 4.3582928E-05 9.7579956E-03 at 50iterations finished qdiffx linear iterations at : 08:26:44 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 4.3582928E-05 9.7579956E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 08:26:45 3.437u 0.169s 0:03.88 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 08:26:45 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5868 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.446018 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 1.446018 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.985961 assigned positive charge : 881.0883 centred at (gu) : 90.65178 89.21953 87.51153 assigned negative charge : -886.0815 centred at (gu) : 91.01390 89.17272 87.41190 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 97685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51578 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26530 mr = 66492 m= 1845 mr = 17105 m= 26 mr = 671 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1338 time to turn everything in is 0.6700000 number of dielectric boundary points 41818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 830 ## 25 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 41895 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) : 0.4820060 object centre at (A) : -18.39800 -3.745501 61.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1279095E-02 -3.8712183E-03 midg,1,midg; midg,igrid,midg 6.4342888E-04 1.9668282E-03 1,midg,midg; igrid,midg,midg 5.4890630E-03 -1.1717415E-02 gauss-seidel spectral radius is 0.9979612 estimated iterations to convergence 176 setup time was (sec) 0.9500000 now iterating at: 08:26:46 rms-change max change #iterations 3.742077 144.2236 at 10iterations 1.479598 52.86260 at 20iterations 0.5862217 19.25995 at 30iterations 0.2324934 7.284910 at 40iterations 9.2237063E-02 2.969567 at 50iterations 3.6743395E-02 1.287094 at 60iterations 1.4630280E-02 0.4911523 at 70iterations 5.8732578E-03 0.2020340 at 80iterations 2.3908014E-03 7.6786280E-02 at 90iterations 1.0066380E-03 3.8375854E-02 at 100iterations 4.5268942E-04 1.8424988E-02 at 110iterations 2.2380197E-04 8.8105202E-03 at 120iterations finished qdiffx linear iterations at : 08:26:52 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 2.2380197E-04 8.8105202E-03 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 08:26:53 7.357u 0.188s 0:07.91 95.1% 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 Sun Oct 9 2011 at 08:26:53 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5868 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.169027 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 2.169027 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.985961 assigned positive charge : 881.0883 centred at (gu) : 90.97732 88.82893 86.26685 assigned negative charge : -886.0815 centred at (gu) : 91.52091 88.75905 86.11793 start vw surface at 0.2300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 228238 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51578 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 98246 mr = 164389 m= 21981 mr = 75410 m= 2446 mr = 15294 m= 71 mr = 1341 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 4426 time to turn everything in is 1.600000 number of dielectric boundary points 94544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 45349 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) : 1.446018 object centre at (A) : -18.39800 -3.745501 61.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2385026 -0.1173721 midg,1,midg; midg,igrid,midg 4.2398740E-02 4.7091670E-02 1,midg,midg; igrid,midg,midg 0.1936893 -0.1798191 gauss-seidel spectral radius is 0.9991482 estimated iterations to convergence 271 setup time was (sec) 1.900000 now iterating at: 08:26:55 rms-change max change #iterations 10.61265 278.7954 at 10iterations 6.065555 143.7324 at 20iterations 3.453423 89.53747 at 30iterations 1.958610 41.38715 at 40iterations 1.102628 23.95384 at 50iterations 0.6213883 14.41906 at 60iterations 0.3484654 6.915833 at 70iterations 0.1945370 3.690729 at 80iterations 0.1088224 2.255660 at 90iterations 6.0713563E-02 1.249103 at 100iterations 3.3806235E-02 0.6619234 at 110iterations 1.8853474E-02 0.3574677 at 120iterations 1.0485212E-02 0.1998965 at 130iterations 5.8464282E-03 0.1012058 at 140iterations 3.2628349E-03 6.1500072E-02 at 150iterations 1.8244220E-03 3.1097412E-02 at 160iterations 1.0247396E-03 1.8257141E-02 at 170iterations 5.8175816E-04 1.0192871E-02 at 180iterations finished qdiffx linear iterations at : 08:27:05 total time elapsed so far: 11.82000 # loops : 180 mean,max change (kT/e) : 5.8175816E-04 1.0192871E-02 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 08:27:05 12.002u 0.200s 0:12.48 97.7% 0+0k 0+0io 0pf+0w