Mon Oct 10 16:04:52 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 Mon Oct 10 2011 at 16:04:52 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4290 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN9 979 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5492217 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): 7.375000 58.97300 ymin,ymax (A): -29.58500 34.30400 zmin,zma (A): -29.24700 35.57200 x,y,z range (A): 51.59800 63.88900 64.81900 scale (grids/A): 0.5492217 object centre (A): 33.17400 2.359501 3.162501 number of atom coordinates read : 4290 total number of charged atoms : 4183 net assigned charge : 7.606029 assigned positive charge : 649.1540 centred at (gu) : 89.81912 89.60234 88.73560 assigned negative charge : -641.5513 centred at (gu) : 89.79487 89.58091 88.74878 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8488 nv = 96 ne = 84 npr = 86327 no. pairs analyzed = 86327 no. exposed pairs = 5309 no. arc points = 36263 no. surface atoms = 1790 nbur = 2500 mkacc time = 0.1900000 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 = 1.568000 m= 339 mr = 4642 m= 0 mr = 16 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.4100000 number of dielectric boundary points 4169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3708 ## 456 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 11184 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2181168E-10 2.9296737E-10 midg,1,midg; midg,igrid,midg 3.3277969E-10 6.9647038E-10 1,midg,midg; igrid,midg,midg 2.8449440E-10 7.6285628E-10 gauss-seidel spectral radius is 0.9830035 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 16:04:53 rms-change max change #iterations 9.3250744E-02 12.93314 at 10iterations 6.5596239E-03 0.9100456 at 20iterations 5.8577769E-04 0.1026096 at 30iterations 1.2321587E-04 2.5072098E-02 at 40iterations 4.0878378E-05 6.9580078E-03 at 50iterations finished qdiffx linear iterations at : 16:04:56 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.0878378E-05 6.9580078E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 16:04:56 3.398u 0.163s 0:04.03 88.0% 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 Mon Oct 10 2011 at 16:04:56 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4290 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN9 979 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.647665 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): 7.375000 58.97300 ymin,ymax (A): -29.58500 34.30400 zmin,zma (A): -29.24700 35.57200 x,y,z range (A): 51.59800 63.88900 64.81900 scale (grids/A): 1.647665 object centre (A): 33.17400 2.359501 3.162501 number of atom coordinates read : 4290 total number of charged atoms : 4183 net assigned charge : 7.606029 assigned positive charge : 649.1540 centred at (gu) : 89.45605 88.80562 86.20524 assigned negative charge : -641.5513 centred at (gu) : 89.38396 88.74216 86.24593 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 94462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36263 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30678 mr = 66761 m= 3442 mr = 21356 m= 94 mr = 1757 m= 0 mr = 10 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 572 time to turn everything in is 0.6300000 number of dielectric boundary points 38792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 411 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 32121 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) : 0.5492217 object centre at (A) : 33.17400 2.359501 3.162501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7649181E-02 -3.0172146E-03 midg,1,midg; midg,igrid,midg 1.7395994E-02 1.7222375E-02 1,midg,midg; igrid,midg,midg 4.0047998E-03 2.3937498E-03 gauss-seidel spectral radius is 0.9983547 estimated iterations to convergence 196 setup time was (sec) 0.9100000 now iterating at: 16:04:57 rms-change max change #iterations 4.204548 156.5219 at 10iterations 1.827073 56.87323 at 20iterations 0.7975204 24.90254 at 30iterations 0.3478678 10.27828 at 40iterations 0.1513117 4.357250 at 50iterations 6.5982126E-02 2.084411 at 60iterations 2.8944906E-02 0.8969765 at 70iterations 1.2626840E-02 0.3867722 at 80iterations 5.5125467E-03 0.1648560 at 90iterations 2.4248676E-03 7.6179504E-02 at 100iterations 1.0724956E-03 3.1173706E-02 at 110iterations 4.8290016E-04 1.4519691E-02 at 120iterations finished qdiffx linear iterations at : 16:05:04 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 4.8290016E-04 1.4519691E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 16:05:04 7.643u 0.213s 0:08.20 95.7% 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 Mon Oct 10 2011 at 16:05:05 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4290 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN9 979 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.471498 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): 7.375000 58.97300 ymin,ymax (A): -29.58500 34.30400 zmin,zma (A): -29.24700 35.57200 x,y,z range (A): 51.59800 63.88900 64.81900 scale (grids/A): 2.471498 object centre (A): 33.17400 2.359501 3.162501 number of atom coordinates read : 4290 total number of charged atoms : 4183 net assigned charge : 7.606029 assigned positive charge : 649.1540 centred at (gu) : 89.18360 88.20809 84.30751 assigned negative charge : -641.5513 centred at (gu) : 89.07568 88.11308 84.36890 start vw surface at 0.2100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 220007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36263 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105332 mr = 163600 m= 31204 mr = 83769 m= 5502 mr = 23708 m= 465 mr = 3667 m= 10 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 1948 time to turn everything in is 1.620000 number of dielectric boundary points 87573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 33424 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) : 1.647665 object centre at (A) : 33.17400 2.359501 3.162501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4385756 -8.2269318E-02 midg,1,midg; midg,igrid,midg 0.3330190 0.2222876 1,midg,midg; igrid,midg,midg 5.1499967E-02 3.4684055E-02 gauss-seidel spectral radius is 0.9992253 estimated iterations to convergence 284 setup time was (sec) 1.920000 now iterating at: 16:05:07 rms-change max change #iterations 10.85323 314.6003 at 10iterations 6.359111 182.5165 at 20iterations 3.705099 83.46632 at 30iterations 2.152702 46.93369 at 40iterations 1.242577 23.60674 at 50iterations 0.7158136 15.44911 at 60iterations 0.4119143 7.256871 at 70iterations 0.2361948 4.411818 at 80iterations 0.1353901 2.433636 at 90iterations 7.7249102E-02 1.302621 at 100iterations 4.4077244E-02 0.8511548 at 110iterations 2.5195839E-02 0.4319687 at 120iterations 1.4394868E-02 0.2436523 at 130iterations 8.2209082E-03 0.1390724 at 140iterations 4.6941610E-03 8.7801933E-02 at 150iterations 2.6971246E-03 4.6386719E-02 at 160iterations 1.5594354E-03 2.9045105E-02 at 170iterations 9.1268343E-04 1.7540932E-02 at 180iterations finished qdiffx linear iterations at : 16:05:17 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 9.1268343E-04 1.7540932E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 16:05:18 12.592u 0.216s 0:13.10 97.7% 0+0k 0+0io 0pf+0w