Mon Oct 10 14:23:44 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 Mon Oct 10 2011 at 14:23:44 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6310266 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): -7.986000 44.16000 ymin,ymax (A): 4.247000 60.66300 zmin,zma (A): -14.44900 36.75400 x,y,z range (A): 52.14600 56.41600 51.20300 scale (grids/A): 0.6310266 object centre (A): 18.08700 32.45500 11.15250 number of atom coordinates read : 2400 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 350.8482 centred at (gu) : 90.00086 89.30389 90.00453 assigned negative charge : -354.8485 centred at (gu) : 89.75071 89.36414 90.02267 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6526 nv = 96 ne = 84 npr = 48342 no. pairs analyzed = 48342 no. exposed pairs = 3208 no. arc points = 22753 no. surface atoms = 1081 nbur = 1319 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3341 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2219 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9832650E-09 -6.0113545E-09 midg,1,midg; midg,igrid,midg 6.1467598E-10 -8.2177101E-09 1,midg,midg; igrid,midg,midg -2.5900858E-08 1.5771095E-08 gauss-seidel spectral radius is 0.9869815 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 14:23:45 rms-change max change #iterations 0.1300626 26.48582 at 10iterations 1.2369504E-02 1.921499 at 20iterations 1.1781959E-03 0.1809559 at 30iterations 1.1181397E-04 1.6681671E-02 at 40iterations 1.1016246E-05 1.6305447E-03 at 50iterations finished qdiffx linear iterations at : 14:23:47 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1016246E-05 1.6305447E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:23:48 3.345u 0.167s 0:04.12 84.9% 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 Mon Oct 10 2011 at 14:23:48 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.893080 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): -7.986000 44.16000 ymin,ymax (A): 4.247000 60.66300 zmin,zma (A): -14.44900 36.75400 x,y,z range (A): 52.14600 56.41600 51.20300 scale (grids/A): 1.893080 object centre (A): 18.08700 32.45500 11.15250 number of atom coordinates read : 2400 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 350.8482 centred at (gu) : 90.00222 87.91142 90.01354 assigned negative charge : -354.8485 centred at (gu) : 89.25202 88.09200 90.06767 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22753 grid for indexing accessible points = 1.400000 m= 24184 mr = 46925 m= 3521 mr = 17083 m= 203 mr = 1919 m= 6 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3400000 number of dielectric boundary points 32058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17640 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) : 0.6310266 object centre at (A) : 18.08700 32.45500 11.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9073300E-03 -2.0299504E-02 midg,1,midg; midg,igrid,midg 6.9155106E-03 -1.0546350E-02 1,midg,midg; igrid,midg,midg -4.6138272E-02 1.6279424E-02 gauss-seidel spectral radius is 0.9986068 estimated iterations to convergence 212 setup time was (sec) 0.5700000 now iterating at: 14:23:49 rms-change max change #iterations 3.936519 161.9457 at 10iterations 1.825509 74.73859 at 20iterations 0.8440482 27.51559 at 30iterations 0.3918183 15.46790 at 40iterations 0.1815626 5.438946 at 50iterations 8.4395707E-02 2.887904 at 60iterations 3.9177872E-02 1.264736 at 70iterations 1.8167729E-02 0.6130142 at 80iterations 8.4228255E-03 0.2839050 at 90iterations 3.9148405E-03 0.1401405 at 100iterations 1.8180551E-03 5.8479309E-02 at 110iterations 8.4416161E-04 2.6462555E-02 at 120iterations finished qdiffx linear iterations at : 14:23:56 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 8.4416161E-04 2.6462555E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 14:23:57 7.719u 0.201s 0:08.40 94.1% 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 14:23:57 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.839620 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): -7.986000 44.16000 ymin,ymax (A): 4.247000 60.66300 zmin,zma (A): -14.44900 36.75400 x,y,z range (A): 52.14600 56.41600 51.20300 scale (grids/A): 2.839620 object centre (A): 18.08700 32.45500 11.15250 number of atom coordinates read : 2400 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 350.8482 centred at (gu) : 90.00320 86.86706 90.01997 assigned negative charge : -354.8485 centred at (gu) : 88.87796 87.13802 90.10137 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22753 grid for indexing accessible points = 1.400000 m= 79156 mr = 113886 m= 27149 mr = 63360 m= 6015 mr = 20923 m= 840 mr = 4039 m= 67 mr = 525 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.9100000 number of dielectric boundary points 72275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 17927 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) : 1.893080 object centre at (A) : 18.08700 32.45500 11.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2170440E-02 -0.3054141 midg,1,midg; midg,igrid,midg 4.6462379E-02 -9.3968250E-02 1,midg,midg; igrid,midg,midg -0.4595419 0.1000005 gauss-seidel spectral radius is 0.9992565 estimated iterations to convergence 289 setup time was (sec) 1.150000 now iterating at: 14:23:58 rms-change max change #iterations 9.518651 495.2332 at 10iterations 5.619925 139.7957 at 20iterations 3.276156 72.95347 at 30iterations 1.910786 47.67459 at 40iterations 1.105997 23.80919 at 50iterations 0.6409937 15.34553 at 60iterations 0.3707583 7.444633 at 70iterations 0.2133205 4.493329 at 80iterations 0.1227881 2.334453 at 90iterations 7.0792928E-02 1.334803 at 100iterations 4.0677898E-02 0.8504362 at 110iterations 2.3338681E-02 0.4416122 at 120iterations 1.3402869E-02 0.2772026 at 130iterations 7.6893577E-03 0.1484604 at 140iterations 4.4275159E-03 8.4697723E-02 at 150iterations 2.5432417E-03 4.8018456E-02 at 160iterations 1.4578375E-03 2.7877808E-02 at 170iterations 8.3602703E-04 1.6929626E-02 at 180iterations finished qdiffx linear iterations at : 14:24:09 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 8.3602703E-04 1.6929626E-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 14:24:10 12.605u 0.194s 0:13.42 95.3% 0+0k 0+0io 0pf+0w