Sun Oct 9 23:35:18 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 23:35:18 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 = 2981 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: 0.5983998 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): -6.661000 52.83100 ymin,ymax (A): -3.785000 50.93200 zmin,zma (A): 26.94900 82.64400 x,y,z range (A): 59.49200 54.71700 55.69500 scale (grids/A): 0.5983998 object centre (A): 23.08500 23.57350 54.79650 number of atom coordinates read : 2981 total number of charged atoms : 2892 net assigned charge : 0.5000062 assigned positive charge : 456.7871 centred at (gu) : 89.66737 91.99642 90.41934 assigned negative charge : -456.2882 centred at (gu) : 89.71746 91.91113 90.54591 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7307 nv = 96 ne = 84 npr = 56535 no. pairs analyzed = 56535 no. exposed pairs = 4152 no. arc points = 30267 no. surface atoms = 1372 nbur = 1609 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3582 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3065 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9148 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7354147E-09 -5.5948548E-09 midg,1,midg; midg,igrid,midg -2.1198292E-09 5.7097553E-09 1,midg,midg; igrid,midg,midg 2.3439395E-09 -1.7593168E-09 gauss-seidel spectral radius is 0.9855935 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 23:35:19 rms-change max change #iterations 0.1163690 16.38672 at 10iterations 9.7020241E-03 1.493205 at 20iterations 8.2289963E-04 0.1355734 at 30iterations 6.8710804E-05 1.0045052E-02 at 40iterations 6.0161128E-06 9.2250109E-04 at 50iterations finished qdiffx linear iterations at : 23:35:22 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.0161128E-06 9.2250109E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 23:35:22 3.485u 0.165s 0:03.99 91.2% 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 Sun Oct 9 2011 at 23:35:22 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 = 2981 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: 1.795199 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): -6.661000 52.83100 ymin,ymax (A): -3.785000 50.93200 zmin,zma (A): 26.94900 82.64400 x,y,z range (A): 59.49200 54.71700 55.69500 scale (grids/A): 1.795199 object centre (A): 23.08500 23.57350 54.79650 number of atom coordinates read : 2981 total number of charged atoms : 2892 net assigned charge : 0.5000062 assigned positive charge : 456.7871 centred at (gu) : 89.00148 95.98849 91.25702 assigned negative charge : -456.2882 centred at (gu) : 89.15219 95.73312 91.63755 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30267 grid for indexing accessible points = 1.400000 m= 25474 mr = 51223 m= 3383 mr = 17157 m= 159 mr = 1703 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 0.3900000 number of dielectric boundary points 37533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 22544 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) : 0.5983998 object centre at (A) : 23.08500 23.57350 54.79650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9762706E-03 -1.7192487E-02 midg,1,midg; midg,igrid,midg -4.5942338E-03 -1.4617789E-03 1,midg,midg; igrid,midg,midg -4.6271142E-03 -1.0525121E-02 gauss-seidel spectral radius is 0.9985338 estimated iterations to convergence 207 setup time was (sec) 0.6100000 now iterating at: 23:35:23 rms-change max change #iterations 4.125800 155.4440 at 10iterations 1.868506 63.52798 at 20iterations 0.8484110 28.50579 at 30iterations 0.3842040 12.70174 at 40iterations 0.1747056 5.669185 at 50iterations 7.9443939E-02 2.529290 at 60iterations 3.6035780E-02 1.180128 at 70iterations 1.6400507E-02 0.5731754 at 80iterations 7.4396287E-03 0.2525673 at 90iterations 3.3906759E-03 0.1183090 at 100iterations 1.5446738E-03 4.8919678E-02 at 110iterations 7.0417585E-04 2.4053574E-02 at 120iterations finished qdiffx linear iterations at : 23:35:30 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 7.0417585E-04 2.4053574E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 23:35:31 7.921u 0.192s 0:08.63 93.9% 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 23:35:31 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 = 2981 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: 2.692799 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): -6.661000 52.83100 ymin,ymax (A): -3.785000 50.93200 zmin,zma (A): 26.94900 82.64400 x,y,z range (A): 59.49200 54.71700 55.69500 scale (grids/A): 2.692799 object centre (A): 23.08500 23.57350 54.79650 number of atom coordinates read : 2981 total number of charged atoms : 2892 net assigned charge : 0.5000062 assigned positive charge : 456.7871 centred at (gu) : 88.50217 98.98251 91.88526 assigned negative charge : -456.2882 centred at (gu) : 88.72810 98.59974 92.45625 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 182370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30267 grid for indexing accessible points = 1.400000 m= 85057 mr = 126030 m= 27023 mr = 65948 m= 5559 mr = 19929 m= 604 mr = 3573 m= 17 mr = 281 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2220 time to turn everything in is 0.9500000 number of dielectric boundary points 84867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 23128 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) : 1.795199 object centre at (A) : 23.08500 23.57350 54.79650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1127330E-02 -0.2235358 midg,1,midg; midg,igrid,midg -5.6173336E-02 -0.1291772 1,midg,midg; igrid,midg,midg -9.4202027E-02 -0.2947834 gauss-seidel spectral radius is 0.9992635 estimated iterations to convergence 291 setup time was (sec) 1.190000 now iterating at: 23:35:32 rms-change max change #iterations 10.24796 297.3705 at 10iterations 6.142511 168.0830 at 20iterations 3.636057 85.62834 at 30iterations 2.148187 50.91698 at 40iterations 1.257683 30.84018 at 50iterations 0.7336873 14.40811 at 60iterations 0.4275867 8.364230 at 70iterations 0.2477924 4.699471 at 80iterations 0.1437720 2.788904 at 90iterations 8.3353311E-02 1.679527 at 100iterations 4.8207920E-02 1.017778 at 110iterations 2.7845927E-02 0.5264702 at 120iterations 1.6073912E-02 0.3043556 at 130iterations 9.2649721E-03 0.1797295 at 140iterations 5.3395927E-03 0.1094851 at 150iterations 3.0751161E-03 6.3617706E-02 at 160iterations 1.7735835E-03 3.3662796E-02 at 170iterations 1.0205861E-03 2.2163391E-02 at 180iterations finished qdiffx linear iterations at : 23:35:44 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 1.0205861E-03 2.2163391E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 23:35:44 12.605u 0.206s 0:13.09 97.7% 0+0k 0+0io 0pf+0w