Tue Oct 11 03:41:08 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 03:41:08 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: ZN3 302 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6060296 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): -11.05700 37.19500 ymin,ymax (A): -27.15600 21.24700 zmin,zma (A): -13.27700 45.46600 x,y,z range (A): 48.25200 48.40300 58.74300 scale (grids/A): 0.6060296 object centre (A): 13.06900 -2.954500 16.09450 number of atom coordinates read : 3211 total number of charged atoms : 2793 net assigned charge : 1.362021 assigned positive charge : 450.1953 centred at (gu) : 89.87727 90.91115 92.24776 assigned negative charge : -448.8341 centred at (gu) : 89.64469 90.85784 92.14180 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7007 nv = 96 ne = 84 npr = 60659 no. pairs analyzed = 60659 no. exposed pairs = 3417 no. arc points = 23793 no. surface atoms = 1164 nbur = 2047 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3976 m= 0 mr = 27 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.3500000 number of dielectric boundary points 3324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2461 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8862 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8971656E-09 9.8456994E-09 midg,1,midg; midg,igrid,midg -1.7242657E-09 4.0001682E-09 1,midg,midg; igrid,midg,midg -1.1808262E-08 1.1675170E-08 gauss-seidel spectral radius is 0.9859272 estimated iterations to convergence 69 setup time was (sec) 0.6400000 now iterating at: 03:41:09 rms-change max change #iterations 0.1255508 19.42142 at 10iterations 1.1072724E-02 1.507584 at 20iterations 1.0070263E-03 0.1716118 at 30iterations 1.1812483E-04 1.9310951E-02 at 40iterations 2.5751391E-05 5.2928925E-03 at 50iterations finished qdiffx linear iterations at : 03:41:13 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 2.5751391E-05 5.2928925E-03 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 03:41:13 4.566u 0.389s 0:05.55 89.0% 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 Tue Oct 11 2011 at 03:41:13 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: ZN3 302 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.818089 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): -11.05700 37.19500 ymin,ymax (A): -27.15600 21.24700 zmin,zma (A): -13.27700 45.46600 x,y,z range (A): 48.25200 48.40300 58.74300 scale (grids/A): 1.818089 object centre (A): 13.06900 -2.954500 16.09450 number of atom coordinates read : 3211 total number of charged atoms : 2793 net assigned charge : 1.362021 assigned positive charge : 450.1953 centred at (gu) : 89.63078 92.73275 96.74274 assigned negative charge : -448.8341 centred at (gu) : 88.93362 92.57320 96.42511 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23793 grid for indexing accessible points = 1.400000 m= 27055 mr = 54064 m= 3657 mr = 20295 m= 172 mr = 2172 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2637 time to turn everything in is 0.6300000 number of dielectric boundary points 30781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21779 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) : 0.6060296 object centre at (A) : 13.06900 -2.954500 16.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4742265E-02 2.9537319E-03 midg,1,midg; midg,igrid,midg 4.3687765E-03 1.5611600E-03 1,midg,midg; igrid,midg,midg -8.2293525E-03 3.8184762E-02 gauss-seidel spectral radius is 0.9985321 estimated iterations to convergence 207 setup time was (sec) 0.9700000 now iterating at: 03:41:15 rms-change max change #iterations 4.245066 198.9090 at 10iterations 1.936029 80.20364 at 20iterations 0.8828578 27.53757 at 30iterations 0.4022367 13.18730 at 40iterations 0.1834527 5.958921 at 50iterations 8.3670363E-02 2.605782 at 60iterations 3.8324811E-02 1.122074 at 70iterations 1.7495276E-02 0.5399456 at 80iterations 8.0035264E-03 0.2580929 at 90iterations 3.6590833E-03 0.1226082 at 100iterations 1.6829438E-03 5.4054260E-02 at 110iterations 7.7428581E-04 2.3269653E-02 at 120iterations finished qdiffx linear iterations at : 03:41:24 total time elapsed so far: 10.55000 # loops : 120 mean,max change (kT/e) : 7.7428581E-04 2.3269653E-02 energy calculations done at 10.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.72000 DelPhi exited at 03:41:25 10.728u 0.440s 0:11.65 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 Tue Oct 11 2011 at 03:41:25 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: ZN3 302 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.727133 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): -11.05700 37.19500 ymin,ymax (A): -27.15600 21.24700 zmin,zma (A): -13.27700 45.46600 x,y,z range (A): 48.25200 48.40300 58.74300 scale (grids/A): 2.727133 object centre (A): 13.06900 -2.954500 16.09450 number of atom coordinates read : 3211 total number of charged atoms : 2793 net assigned charge : 1.362021 assigned positive charge : 450.1953 centred at (gu) : 89.44596 94.09906 100.1136 assigned negative charge : -448.8341 centred at (gu) : 88.40044 93.85970 99.63753 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 176962 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23793 grid for indexing accessible points = 1.400000 m= 89469 mr = 131070 m= 30625 mr = 73996 m= 6285 mr = 24667 m= 751 mr = 4570 m= 39 mr = 452 m= 0 mr = 12 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 8733 time to turn everything in is 1.600000 number of dielectric boundary points 69364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 22340 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) : 1.818089 object centre at (A) : 13.06900 -2.954500 16.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.074199 0.2356098 midg,1,midg; midg,igrid,midg 4.9032524E-02 -5.8105927E-02 1,midg,midg; igrid,midg,midg -6.8307705E-02 0.3730762 gauss-seidel spectral radius is 0.9992295 estimated iterations to convergence 284 setup time was (sec) 1.940000 now iterating at: 03:41:27 rms-change max change #iterations 10.04365 351.6605 at 10iterations 5.788469 135.2595 at 20iterations 3.317821 75.73163 at 30iterations 1.904395 45.92683 at 40iterations 1.087255 22.95447 at 50iterations 0.6207678 13.43279 at 60iterations 0.3534241 7.241348 at 70iterations 0.2021736 3.544350 at 80iterations 0.1150794 2.338945 at 90iterations 6.5457754E-02 1.304121 at 100iterations 3.7409469E-02 0.6940985 at 110iterations 2.1266203E-02 0.3904095 at 120iterations 1.2112886E-02 0.2143211 at 130iterations 6.9118952E-03 0.1261249 at 140iterations 3.9477921E-03 7.5899124E-02 at 150iterations 2.2662552E-03 4.1315079E-02 at 160iterations 1.3046979E-03 2.4441719E-02 at 170iterations 7.5744960E-04 1.4912605E-02 at 180iterations finished qdiffx linear iterations at : 03:41:44 total time elapsed so far: 18.06000 # loops : 180 mean,max change (kT/e) : 7.5744960E-04 1.4912605E-02 energy calculations done at 18.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.23000 DelPhi exited at 03:41:44 18.231u 0.454s 0:19.36 96.4% 0+0k 0+0io 0pf+0w