Mon Oct 10 11:09:45 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 11:09:45 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7415431 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): -21.00800 24.21000 ymin,ymax (A): -8.080000 36.15200 zmin,zma (A): -3.643000 44.36500 x,y,z range (A): 45.21800 44.23199 48.00800 scale (grids/A): 0.7415431 object centre (A): 1.601000 14.03600 20.36100 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 318.2999 centred at (gu) : 89.08269 90.52103 90.21896 assigned negative charge : -324.5720 centred at (gu) : 89.11723 90.60265 90.41077 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7940 nv = 96 ne = 84 npr = 43739 no. pairs analyzed = 43739 no. exposed pairs = 2700 no. arc points = 19230 no. surface atoms = 908 nbur = 1209 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4386 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.3000000 number of dielectric boundary points 3980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1582 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8462 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2888917E-08 -3.3432084E-07 midg,1,midg; midg,igrid,midg -2.5342727E-08 -2.2106724E-07 1,midg,midg; igrid,midg,midg -9.0101956E-08 -1.2708892E-07 gauss-seidel spectral radius is 0.9905241 estimated iterations to convergence 83 setup time was (sec) 0.5700000 now iterating at: 11:09:46 rms-change max change #iterations 0.2487103 43.87202 at 10iterations 3.3746269E-02 4.652276 at 20iterations 4.5541357E-03 0.6740761 at 30iterations 6.1750552E-04 7.4661255E-02 at 40iterations 8.3707841E-05 1.1003971E-02 at 50iterations finished qdiffx linear iterations at : 11:09:50 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 8.3707841E-05 1.1003971E-02 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 11:09:50 4.014u 0.258s 0:04.75 89.6% 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 11:09:50 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.224629 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): -21.00800 24.21000 ymin,ymax (A): -8.080000 36.15200 zmin,zma (A): -3.643000 44.36500 x,y,z range (A): 45.21800 44.23199 48.00800 scale (grids/A): 2.224629 object centre (A): 1.601000 14.03600 20.36100 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 318.2999 centred at (gu) : 87.24806 91.56319 90.65697 assigned negative charge : -324.5720 centred at (gu) : 87.35170 91.80781 91.23242 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 83891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19230 grid for indexing accessible points = 1.400000 m= 33715 mr = 57728 m= 7213 mr = 25702 m= 768 mr = 5027 m= 22 mr = 454 m= 0 mr = 8 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 4396 time to turn everything in is 0.7700000 number of dielectric boundary points 36690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 15756 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) : 0.7415431 object centre at (A) : 1.601000 14.03600 20.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4185561E-03 -0.1375059 midg,1,midg; midg,igrid,midg -2.4652692E-02 -3.4628104E-02 1,midg,midg; igrid,midg,midg 3.8890671E-03 -1.1823450E-02 gauss-seidel spectral radius is 0.9989313 estimated iterations to convergence 242 setup time was (sec) 1.060000 now iterating at: 11:09:52 rms-change max change #iterations 5.117553 226.5930 at 10iterations 2.598958 78.23228 at 20iterations 1.326023 37.22916 at 30iterations 0.6785946 21.45570 at 40iterations 0.3448572 9.625237 at 50iterations 0.1764386 4.819344 at 60iterations 9.0132423E-02 2.454937 at 70iterations 4.5857541E-02 1.387132 at 80iterations 2.3491275E-02 0.6530399 at 90iterations 1.1983409E-02 0.3611569 at 100iterations 6.1140023E-03 0.1763134 at 110iterations 3.1164917E-03 8.5536599E-02 at 120iterations finished qdiffx linear iterations at : 11:10:00 total time elapsed so far: 9.400000 # loops : 120 mean,max change (kT/e) : 3.1164917E-03 8.5536599E-02 energy calculations done at 9.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 11:10:00 9.586u 0.288s 0:10.14 97.2% 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 11:10:00 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.336944 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): -21.00800 24.21000 ymin,ymax (A): -8.080000 36.15200 zmin,zma (A): -3.643000 44.36500 x,y,z range (A): 45.21800 44.23199 48.00800 scale (grids/A): 3.336944 object centre (A): 1.601000 14.03600 20.36100 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 318.2999 centred at (gu) : 85.87215 92.34466 90.98545 assigned negative charge : -324.5720 centred at (gu) : 86.02759 92.71167 91.84855 start vw surface at 0.1400000 fill in re-entrant regions at 1.110000 boundary points on vw surface= 192929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19230 grid for indexing accessible points = 1.400000 m= 102989 mr = 138848 m= 44271 mr = 85279 m= 13891 mr = 37043 m= 3166 mr = 11068 m= 463 mr = 2458 m= 16 mr = 316 m= 0 mr = 4 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 14324 time to turn everything in is 2.480000 number of dielectric boundary points 82709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.640000 number of grid points assigned charge 15824 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) : 2.224629 object centre at (A) : 1.601000 14.03600 20.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2488574E-02 -1.294418 midg,1,midg; midg,igrid,midg -0.2261304 -0.1543978 1,midg,midg; igrid,midg,midg 8.3121158E-02 -0.1824587 gauss-seidel spectral radius is 0.9993194 estimated iterations to convergence 302 setup time was (sec) 2.810000 now iterating at: 11:10:04 rms-change max change #iterations 11.01168 311.0906 at 10iterations 6.458232 126.1903 at 20iterations 3.800622 63.25855 at 30iterations 2.226032 36.60490 at 40iterations 1.306352 21.33570 at 50iterations 0.7675081 13.39378 at 60iterations 0.4490411 7.400726 at 70iterations 0.2640267 4.400546 at 80iterations 0.1548165 2.564030 at 90iterations 9.0670660E-02 1.428049 at 100iterations 5.3258639E-02 0.8592644 at 110iterations 3.1260855E-02 0.5607758 at 120iterations 1.8323425E-02 0.3259010 at 130iterations 1.0770249E-02 0.1679960 at 140iterations 6.3192975E-03 9.7826958E-02 at 150iterations 3.7123470E-03 6.0153961E-02 at 160iterations 2.1739122E-03 3.7460327E-02 at 170iterations 1.2784908E-03 2.0856857E-02 at 180iterations finished qdiffx linear iterations at : 11:10:17 total time elapsed so far: 16.71000 # loops : 180 mean,max change (kT/e) : 1.2784908E-03 2.0856857E-02 energy calculations done at 16.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.89000 DelPhi exited at 11:10:18 16.896u 0.314s 0:17.63 97.5% 0+0k 0+0io 0pf+0w