Tue Oct 11 06:11:31 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 06:11:31 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7068541 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): 20.17000 64.03600 ymin,ymax (A): -3.539000 33.47700 zmin,zma (A): 19.62400 69.98800 x,y,z range (A): 43.86600 37.01600 50.36400 scale (grids/A): 0.7068541 object centre (A): 42.10300 14.96900 44.80600 number of atom coordinates read : 2259 total number of charged atoms : 1939 net assigned charge : 6.039011 assigned positive charge : 316.7661 centred at (gu) : 89.79005 89.73528 89.56948 assigned negative charge : -310.7271 centred at (gu) : 89.92234 89.76753 89.52032 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6987 nv = 96 ne = 84 npr = 41727 no. pairs analyzed = 41727 no. exposed pairs = 2530 no. arc points = 17053 no. surface atoms = 852 nbur = 1407 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4019 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1529 ## 129 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7760 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8289680E-08 6.8156680E-08 midg,1,midg; midg,igrid,midg 6.9277220E-08 3.2867497E-08 1,midg,midg; igrid,midg,midg 1.1845177E-07 -1.4215995E-08 gauss-seidel spectral radius is 0.9895653 estimated iterations to convergence 80 setup time was (sec) 0.5000000 now iterating at: 06:11:32 rms-change max change #iterations 0.2040407 28.20477 at 10iterations 2.5631506E-02 3.774399 at 20iterations 3.4100756E-03 0.5080338 at 30iterations 5.6805892E-04 8.2031250E-02 at 40iterations 1.3557333E-04 1.8529892E-02 at 50iterations finished qdiffx linear iterations at : 06:11:34 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.3557333E-04 1.8529892E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:11:35 3.332u 0.228s 0:04.04 87.8% 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 Tue Oct 11 2011 at 06:11:35 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.120562 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): 20.17000 64.03600 ymin,ymax (A): -3.539000 33.47700 zmin,zma (A): 19.62400 69.98800 x,y,z range (A): 43.86600 37.01600 50.36400 scale (grids/A): 2.120562 object centre (A): 42.10300 14.96900 44.80600 number of atom coordinates read : 2259 total number of charged atoms : 1939 net assigned charge : 6.039011 assigned positive charge : 316.7661 centred at (gu) : 89.36999 89.20589 88.70869 assigned negative charge : -310.7271 centred at (gu) : 89.76711 89.30271 88.56108 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17053 grid for indexing accessible points = 1.400000 m= 29951 mr = 53176 m= 5740 mr = 22873 m= 574 mr = 3752 m= 17 mr = 317 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 30769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15268 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) : 0.7068541 object centre at (A) : 42.10300 14.96900 44.80600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4418788E-02 6.1650526E-02 midg,1,midg; midg,igrid,midg 2.5533853E-02 1.1767101E-02 1,midg,midg; igrid,midg,midg 3.6675651E-02 1.2102691E-02 gauss-seidel spectral radius is 0.9988267 estimated iterations to convergence 231 setup time was (sec) 0.8500000 now iterating at: 06:11:36 rms-change max change #iterations 4.602604 186.4038 at 10iterations 2.282272 69.05912 at 20iterations 1.127108 32.86548 at 30iterations 0.5599114 16.73661 at 40iterations 0.2774348 8.865278 at 50iterations 0.1377866 4.323147 at 60iterations 6.8281576E-02 2.217533 at 70iterations 3.3988010E-02 1.122326 at 80iterations 1.6955610E-02 0.5249095 at 90iterations 8.4702065E-03 0.2481651 at 100iterations 4.2567411E-03 0.1358604 at 110iterations 2.1700475E-03 6.2385559E-02 at 120iterations finished qdiffx linear iterations at : 06:11:43 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 2.1700475E-03 6.2385559E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 06:11:43 7.632u 0.216s 0:08.12 96.5% 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 Tue Oct 11 2011 at 06:11:43 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.180844 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): 20.17000 64.03600 ymin,ymax (A): -3.539000 33.47700 zmin,zma (A): 19.62400 69.98800 x,y,z range (A): 43.86600 37.01600 50.36400 scale (grids/A): 3.180844 object centre (A): 42.10300 14.96900 44.80600 number of atom coordinates read : 2259 total number of charged atoms : 1939 net assigned charge : 6.039011 assigned positive charge : 316.7661 centred at (gu) : 89.05515 88.80879 88.06309 assigned negative charge : -310.7271 centred at (gu) : 89.65073 88.95423 87.84169 start vw surface at 0.1500000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 172246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17053 grid for indexing accessible points = 1.400000 m= 93537 mr = 128296 m= 37713 mr = 78068 m= 10799 mr = 31102 m= 2180 mr = 8250 m= 300 mr = 1569 m= 7 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 69291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 15510 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) : 2.120562 object centre at (A) : 42.10300 14.96900 44.80600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2566000 0.5318366 midg,1,midg; midg,igrid,midg 0.2058054 9.7087897E-02 1,midg,midg; igrid,midg,midg 0.2940225 0.2523111 gauss-seidel spectral radius is 0.9992933 estimated iterations to convergence 297 setup time was (sec) 2.120000 now iterating at: 06:11:46 rms-change max change #iterations 10.29687 361.2542 at 10iterations 6.094318 122.7064 at 20iterations 3.600022 68.94536 at 30iterations 2.120840 42.51070 at 40iterations 1.247197 27.04143 at 50iterations 0.7329477 13.37813 at 60iterations 0.4302397 8.231614 at 70iterations 0.2525969 5.354381 at 80iterations 0.1479171 2.601676 at 90iterations 8.6552948E-02 1.515790 at 100iterations 5.0955836E-02 0.8801234 at 110iterations 3.0024603E-02 0.5079904 at 120iterations 1.7863501E-02 0.3540401 at 130iterations 1.0774260E-02 0.2027440 at 140iterations 6.6883275E-03 0.1343231 at 150iterations 4.2848061E-03 8.3007813E-02 at 160iterations 2.9069802E-03 5.6297302E-02 at 170iterations 2.0850331E-03 4.1572571E-02 at 180iterations finished qdiffx linear iterations at : 06:12:00 total time elapsed so far: 16.96000 # loops : 180 mean,max change (kT/e) : 2.0850331E-03 4.1572571E-02 energy calculations done at 16.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.13000 DelPhi exited at 06:12:01 17.134u 0.308s 0:17.75 98.1% 0+0k 0+0io 0pf+0w