Tue Oct 11 08:33:44 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 Tue Oct 11 2011 at 08:33:45 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3260 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5981686 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): 71.53400 122.6050 ymin,ymax (A): -15.92700 36.48800 zmin,zma (A): -28.07900 31.43600 x,y,z range (A): 51.07101 52.41500 59.51500 scale (grids/A): 0.5981686 object centre (A): 97.06950 10.28050 1.678499 number of atom coordinates read : 3260 total number of charged atoms : 3108 net assigned charge : -0.5999879 assigned positive charge : 487.4347 centred at (gu) : 89.75228 90.25932 90.77390 assigned negative charge : -488.0359 centred at (gu) : 89.86312 90.16043 90.70845 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7575 nv = 96 ne = 84 npr = 68242 no. pairs analyzed = 68242 no. exposed pairs = 3710 no. arc points = 25175 no. surface atoms = 1267 nbur = 1993 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 4432 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.4100000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6326632E-09 3.0316973E-09 midg,1,midg; midg,igrid,midg -4.3546833E-09 4.1981454E-09 1,midg,midg; igrid,midg,midg 4.7222373E-09 -4.8675468E-09 gauss-seidel spectral radius is 0.9855822 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 08:33:45 rms-change max change #iterations 0.1201775 17.29463 at 10iterations 1.0813048E-02 1.536736 at 20iterations 1.3419456E-03 0.2095795 at 30iterations 3.5933653E-04 6.6967010E-02 at 40iterations 1.1665835E-04 2.1879196E-02 at 50iterations finished qdiffx linear iterations at : 08:33:49 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.1665835E-04 2.1879196E-02 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 08:33:50 4.193u 0.296s 0:05.08 88.1% 0+0k 0+0io 6pf+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 08:33:50 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3260 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.794506 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): 71.53400 122.6050 ymin,ymax (A): -15.92700 36.48800 zmin,zma (A): -28.07900 31.43600 x,y,z range (A): 51.07101 52.41500 59.51500 scale (grids/A): 1.794506 object centre (A): 97.06950 10.28050 1.678499 number of atom coordinates read : 3260 total number of charged atoms : 3108 net assigned charge : -0.5999879 assigned positive charge : 487.4347 centred at (gu) : 89.25573 90.77675 92.32081 assigned negative charge : -488.0359 centred at (gu) : 89.58905 90.48088 92.12492 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 83527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25175 grid for indexing accessible points = 1.400000 m= 29183 mr = 60371 m= 3845 mr = 21987 m= 161 mr = 2382 m= 0 mr = 45 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2041 time to turn everything in is 0.7200000 number of dielectric boundary points 31931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 24213 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) : 0.5981686 object centre at (A) : 97.06950 10.28050 1.678499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1985199E-02 7.7739242E-03 midg,1,midg; midg,igrid,midg -1.9484138E-02 -1.7443330E-03 1,midg,midg; igrid,midg,midg 2.2091754E-02 -1.9022383E-02 gauss-seidel spectral radius is 0.9985250 estimated iterations to convergence 206 setup time was (sec) 1.030000 now iterating at: 08:33:51 rms-change max change #iterations 4.287752 181.2229 at 10iterations 1.952819 63.75579 at 20iterations 0.8887627 28.10219 at 30iterations 0.4055291 13.96902 at 40iterations 0.1849622 5.949821 at 50iterations 8.4477767E-02 2.554174 at 60iterations 3.8593076E-02 1.205896 at 70iterations 1.7561264E-02 0.5626678 at 80iterations 8.0191614E-03 0.2323606 at 90iterations 3.6992554E-03 0.1083646 at 100iterations 1.7268910E-03 5.7597160E-02 at 110iterations 8.2501478E-04 2.5833130E-02 at 120iterations finished qdiffx linear iterations at : 08:34:00 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 8.2501478E-04 2.5833130E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 08:34:00 9.731u 0.302s 0:10.37 96.7% 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 08:34:00 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3260 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.691758 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): 71.53400 122.6050 ymin,ymax (A): -15.92700 36.48800 zmin,zma (A): -28.07900 31.43600 x,y,z range (A): 51.07101 52.41500 59.51500 scale (grids/A): 2.691758 object centre (A): 97.06950 10.28050 1.678499 number of atom coordinates read : 3260 total number of charged atoms : 3108 net assigned charge : -0.5999879 assigned positive charge : 487.4347 centred at (gu) : 88.88347 91.16483 93.48102 assigned negative charge : -488.0359 centred at (gu) : 89.38338 90.72115 93.18735 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 193713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25175 grid for indexing accessible points = 1.400000 m= 97387 mr = 145857 m= 32508 mr = 81238 m= 6546 mr = 26346 m= 771 mr = 4951 m= 26 mr = 527 m= 0 mr = 10 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 6819 time to turn everything in is 1.860000 number of dielectric boundary points 72022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 24854 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) : 1.794506 object centre at (A) : 97.06950 10.28050 1.678499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4818355 -4.0695865E-02 midg,1,midg; midg,igrid,midg -0.2281533 -0.1163248 1,midg,midg; igrid,midg,midg 0.2592650 -0.2733408 gauss-seidel spectral radius is 0.9992342 estimated iterations to convergence 285 setup time was (sec) 2.190000 now iterating at: 08:34:03 rms-change max change #iterations 10.26511 375.3928 at 10iterations 5.923318 126.0620 at 20iterations 3.418603 72.28149 at 30iterations 1.952934 40.15927 at 40iterations 1.119574 20.05785 at 50iterations 0.6401771 10.93340 at 60iterations 0.3651507 7.436293 at 70iterations 0.2082211 3.847851 at 80iterations 0.1189801 2.186079 at 90iterations 6.7745022E-02 1.210661 at 100iterations 3.8632203E-02 0.7255993 at 110iterations 2.2066537E-02 0.3811178 at 120iterations 1.2591602E-02 0.2202263 at 130iterations 7.2174645E-03 0.1309586 at 140iterations 4.1707782E-03 7.2469711E-02 at 150iterations 2.4341263E-03 4.6394348E-02 at 160iterations 1.4477927E-03 2.7666092E-02 at 170iterations 8.9431385E-04 1.7955780E-02 at 180iterations finished qdiffx linear iterations at : 08:34:17 total time elapsed so far: 16.30000 # loops : 180 mean,max change (kT/e) : 8.9431385E-04 1.7955780E-02 energy calculations done at 16.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.48000 DelPhi exited at 08:34:17 16.481u 0.326s 0:17.30 97.1% 0+0k 0+0io 0pf+0w