Sun Oct 9 13:47:08 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 13:47:09 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 = 2366 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: 0.7072755 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): -1.431000 45.61700 ymin,ymax (A): 36.13200 86.46600 zmin,zma (A): -24.18600 25.24300 x,y,z range (A): 47.04800 50.33400 49.42900 scale (grids/A): 0.7072755 object centre (A): 22.09300 61.29900 0.5285006 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 90.06956 89.97324 91.52365 assigned negative charge : -356.4896 centred at (gu) : 90.20205 90.08072 91.47713 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8094 nv = 96 ne = 84 npr = 47632 no. pairs analyzed = 47632 no. exposed pairs = 2991 no. arc points = 20795 no. surface atoms = 998 nbur = 1368 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 507 mr = 4532 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1868 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8878 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4512832E-09 7.4133901E-08 midg,1,midg; midg,igrid,midg 8.9247450E-08 -3.1816295E-08 1,midg,midg; igrid,midg,midg 1.0111076E-07 -4.7064926E-08 gauss-seidel spectral radius is 0.9896116 estimated iterations to convergence 80 setup time was (sec) 0.6300000 now iterating at: 13:47:10 rms-change max change #iterations 0.2157604 24.25627 at 10iterations 2.6697632E-02 3.773551 at 20iterations 3.8882843E-03 0.6102037 at 30iterations 8.7303878E-04 0.1473389 at 40iterations 2.8166172E-04 4.4620514E-02 at 50iterations finished qdiffx linear iterations at : 13:47:14 total time elapsed so far: 5.480000 # loops : 50 mean,max change (kT/e) : 2.8166172E-04 4.4620514E-02 energy calculations done at 5.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.650000 DelPhi exited at 13:47:15 5.659u 0.459s 0:06.41 95.1% 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 Sun Oct 9 2011 at 13:47:15 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 = 2366 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: 2.121826 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): -1.431000 45.61700 ymin,ymax (A): 36.13200 86.46600 zmin,zma (A): -24.18600 25.24300 x,y,z range (A): 47.04800 50.33400 49.42900 scale (grids/A): 2.121826 object centre (A): 22.09300 61.29900 0.5285006 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 90.20827 89.91947 94.57053 assigned negative charge : -356.4896 centred at (gu) : 90.60619 90.24195 94.43123 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20795 grid for indexing accessible points = 1.400000 m= 33247 mr = 59826 m= 6099 mr = 24821 m= 523 mr = 3926 m= 11 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 315 time to turn everything in is 0.7600000 number of dielectric boundary points 36708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 17648 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) : 0.7072755 object centre at (A) : 22.09300 61.29900 0.5285006 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8140756E-02 2.6578149E-02 midg,1,midg; midg,igrid,midg 9.5066868E-02 -9.0286015E-03 1,midg,midg; igrid,midg,midg 1.0034441E-02 -1.2552974E-02 gauss-seidel spectral radius is 0.9988663 estimated iterations to convergence 235 setup time was (sec) 1.130000 now iterating at: 13:47:17 rms-change max change #iterations 4.990108 193.0165 at 10iterations 2.487292 84.35600 at 20iterations 1.245456 39.30664 at 30iterations 0.6254441 17.26889 at 40iterations 0.3129894 8.190216 at 50iterations 0.1571288 4.245052 at 60iterations 7.8833751E-02 2.302914 at 70iterations 3.9598774E-02 1.165697 at 80iterations 1.9991264E-02 0.6573410 at 90iterations 1.0205488E-02 0.2763824 at 100iterations 5.2727289E-03 0.1604614 at 110iterations 2.7994234E-03 8.8552475E-02 at 120iterations finished qdiffx linear iterations at : 13:47:29 total time elapsed so far: 13.54000 # loops : 120 mean,max change (kT/e) : 2.7994234E-03 8.8552475E-02 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.71000 DelPhi exited at 13:47:30 13.714u 0.521s 0:14.55 97.8% 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 13:47:30 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 = 2366 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: 3.182739 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): -1.431000 45.61700 ymin,ymax (A): 36.13200 86.46600 zmin,zma (A): -24.18600 25.24300 x,y,z range (A): 47.04800 50.33400 49.42900 scale (grids/A): 3.182739 object centre (A): 22.09300 61.29900 0.5285006 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 90.31227 89.87915 96.85553 assigned negative charge : -356.4896 centred at (gu) : 90.90928 90.36279 96.64692 start vw surface at 0.1200000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 197297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20795 grid for indexing accessible points = 1.400000 m= 104817 mr = 144268 m= 41006 mr = 86265 m= 11262 mr = 33342 m= 2143 mr = 8519 m= 257 mr = 1508 m= 12 mr = 173 m= 0 mr = 3 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 1071 time to turn everything in is 2.280000 number of dielectric boundary points 82716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.450000 number of grid points assigned charge 17798 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) : 2.121826 object centre at (A) : 22.09300 61.29900 0.5285006 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8175421E-02 0.3798039 midg,1,midg; midg,igrid,midg 1.342791 -0.2100883 1,midg,midg; igrid,midg,midg 5.6929711E-02 -0.1081412 gauss-seidel spectral radius is 0.9993107 estimated iterations to convergence 300 setup time was (sec) 2.680000 now iterating at: 13:47:33 rms-change max change #iterations 11.20912 347.4769 at 10iterations 6.694023 146.5686 at 20iterations 3.995706 80.35507 at 30iterations 2.378959 43.07499 at 40iterations 1.409637 24.23971 at 50iterations 0.8346249 13.97962 at 60iterations 0.4940577 8.582542 at 70iterations 0.2916603 6.087091 at 80iterations 0.1721169 3.261261 at 90iterations 0.1014940 1.665056 at 100iterations 5.9893258E-02 1.024883 at 110iterations 3.5517361E-02 0.6261311 at 120iterations 2.1144798E-02 0.3788443 at 130iterations 1.2772946E-02 0.2219067 at 140iterations 7.8860354E-03 0.1513405 at 150iterations 5.0717811E-03 9.4532013E-02 at 160iterations 3.4409903E-03 7.1262360E-02 at 170iterations 2.4907503E-03 5.0521851E-02 at 180iterations finished qdiffx linear iterations at : 13:47:53 total time elapsed so far: 23.16000 # loops : 180 mean,max change (kT/e) : 2.4907503E-03 5.0521851E-02 energy calculations done at 23.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.35000 DelPhi exited at 13:47:54 23.356u 0.575s 0:24.25 98.6% 0+0k 0+0io 0pf+0w