Sun Oct 9 02:13:10 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 Sun Oct 9 2011 at 02:13:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 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: 0.6480385 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): -121.3630 -67.85700 ymin,ymax (A): 46.40500 101.3400 zmin,zma (A): 63.54400 107.0240 x,y,z range (A): 53.50600 54.93501 43.48000 scale (grids/A): 0.6480385 object centre (A): -94.61000 73.87250 85.28400 number of atom coordinates read : 2463 total number of charged atoms : 2327 net assigned charge : 10.50002 assigned positive charge : 361.2762 centred at (gu) : 90.41288 88.73656 90.19292 assigned negative charge : -350.7770 centred at (gu) : 90.35990 88.75244 90.09475 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7094 nv = 96 ne = 84 npr = 48952 no. pairs analyzed = 48952 no. exposed pairs = 3295 no. arc points = 23528 no. surface atoms = 1096 nbur = 1367 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 3666 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2273 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8380 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9135807E-09 3.3095933E-08 midg,1,midg; midg,igrid,midg 2.7480672E-08 1.3194443E-08 1,midg,midg; igrid,midg,midg 1.1179901E-08 2.8301615E-08 gauss-seidel spectral radius is 0.9876591 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 02:13:11 rms-change max change #iterations 0.1481525 23.65403 at 10iterations 1.4974739E-02 2.082848 at 20iterations 1.6568248E-03 0.2241383 at 30iterations 2.8793368E-04 3.9033890E-02 at 40iterations 9.2601040E-05 1.5069723E-02 at 50iterations finished qdiffx linear iterations at : 02:13:13 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 9.2601040E-05 1.5069723E-02 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 02:13:13 3.173u 0.172s 0:03.75 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 Sun Oct 9 2011 at 02:13:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 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: 1.944116 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): -121.3630 -67.85700 ymin,ymax (A): 46.40500 101.3400 zmin,zma (A): 63.54400 107.0240 x,y,z range (A): 53.50600 54.93501 43.48000 scale (grids/A): 1.944116 object centre (A): -94.61000 73.87250 85.28400 number of atom coordinates read : 2463 total number of charged atoms : 2327 net assigned charge : 10.50002 assigned positive charge : 361.2762 centred at (gu) : 91.23818 86.20941 90.57826 assigned negative charge : -350.7770 centred at (gu) : 91.07976 86.25723 90.28429 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23528 grid for indexing accessible points = 1.400000 m= 27618 mr = 50291 m= 4694 mr = 19769 m= 358 mr = 2738 m= 5 mr = 121 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 0.5400000 number of dielectric boundary points 35189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18333 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) : 0.6480385 object centre at (A) : -94.61000 73.87250 85.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8711710E-04 2.6272647E-02 midg,1,midg; midg,igrid,midg 4.2325854E-02 3.9721370E-02 1,midg,midg; igrid,midg,midg 2.1130582E-02 5.6779832E-02 gauss-seidel spectral radius is 0.9986891 estimated iterations to convergence 219 setup time was (sec) 0.8400000 now iterating at: 02:13:15 rms-change max change #iterations 4.174857 181.3177 at 10iterations 1.981993 73.32162 at 20iterations 0.9381821 31.86816 at 30iterations 0.4449188 14.86857 at 40iterations 0.2118299 6.782618 at 50iterations 0.1004498 3.428308 at 60iterations 4.7792189E-02 1.490460 at 70iterations 2.2767298E-02 0.6803069 at 80iterations 1.0834703E-02 0.3431635 at 90iterations 5.1536127E-03 0.1689987 at 100iterations 2.4730859E-03 7.3547363E-02 at 110iterations 1.1966267E-03 3.8137436E-02 at 120iterations finished qdiffx linear iterations at : 02:13:22 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 1.1966267E-03 3.8137436E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 02:13:22 8.025u 0.285s 0:08.64 96.0% 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 Sun Oct 9 2011 at 02:13:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 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: 2.916173 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): -121.3630 -67.85700 ymin,ymax (A): 46.40500 101.3400 zmin,zma (A): 63.54400 107.0240 x,y,z range (A): 53.50600 54.93501 43.48000 scale (grids/A): 2.916173 object centre (A): -94.61000 73.87250 85.28400 number of atom coordinates read : 2463 total number of charged atoms : 2327 net assigned charge : 10.50002 assigned positive charge : 361.2762 centred at (gu) : 91.85719 84.31399 90.86734 assigned negative charge : -350.7770 centred at (gu) : 91.61958 84.38588 90.42644 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 174358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23528 grid for indexing accessible points = 1.400000 m= 87156 mr = 122663 m= 32828 mr = 69619 m= 8377 mr = 25749 m= 1447 mr = 5901 m= 122 mr = 899 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 79401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 18616 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) : 1.944116 object centre at (A) : -94.61000 73.87250 85.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7210915E-02 0.2338819 midg,1,midg; midg,igrid,midg 0.4750555 0.7225660 1,midg,midg; igrid,midg,midg 0.2994590 0.5441231 gauss-seidel spectral radius is 0.9992813 estimated iterations to convergence 294 setup time was (sec) 1.730000 now iterating at: 02:13:24 rms-change max change #iterations 9.906063 307.5953 at 10iterations 5.911722 123.8553 at 20iterations 3.490327 72.59157 at 30iterations 2.052397 43.34094 at 40iterations 1.203276 23.10644 at 50iterations 0.7040048 14.66219 at 60iterations 0.4114648 7.713980 at 70iterations 0.2402568 4.830139 at 80iterations 0.1397532 2.608212 at 90iterations 8.1266657E-02 1.681175 at 100iterations 4.7249489E-02 0.8634410 at 110iterations 2.7460303E-02 0.4848857 at 120iterations 1.5977187E-02 0.3026168 at 130iterations 9.2866393E-03 0.1987629 at 140iterations 5.4058712E-03 9.6069336E-02 at 150iterations 3.1496764E-03 5.6481361E-02 at 160iterations 1.8423464E-03 3.3650398E-02 at 170iterations 1.0887289E-03 2.2421837E-02 at 180iterations finished qdiffx linear iterations at : 02:13:35 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.0887289E-03 2.2421837E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 02:13:36 13.198u 0.262s 0:13.73 97.9% 0+0k 0+0io 0pf+0w