Sun Oct 9 09:27:36 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 09:27:37 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 = 2728 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: 0.5731950 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): -79.77600 -31.94200 ymin,ymax (A): -34.74500 27.36300 zmin,zma (A): -51.51000 7.511000 x,y,z range (A): 47.83400 62.10800 59.02100 scale (grids/A): 0.5731950 object centre (A): -55.85900 -3.691002 -21.99950 number of atom coordinates read : 2728 total number of charged atoms : 2584 net assigned charge : 1.000018 assigned positive charge : 404.1206 centred at (gu) : 89.30776 88.95939 88.24914 assigned negative charge : -403.1215 centred at (gu) : 89.32478 89.18815 88.32088 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6027 nv = 96 ne = 84 npr = 52938 no. pairs analyzed = 52938 no. exposed pairs = 3809 no. arc points = 26484 no. surface atoms = 1261 nbur = 1467 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 284 mr = 2988 m= 0 mr = 22 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2635 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7625 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8857034E-09 -6.7969624E-10 midg,1,midg; midg,igrid,midg 4.6690323E-09 -2.8125131E-09 1,midg,midg; igrid,midg,midg 4.4545365E-10 -1.3475444E-10 gauss-seidel spectral radius is 0.9842827 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 09:27:37 rms-change max change #iterations 8.8311404E-02 15.20937 at 10iterations 6.7248493E-03 1.012273 at 20iterations 5.0501962E-04 8.2647324E-02 at 30iterations 3.9060738E-05 6.5383911E-03 at 40iterations 3.4557615E-06 5.5694580E-04 at 50iterations finished qdiffx linear iterations at : 09:27:40 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 3.4557615E-06 5.5694580E-04 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 09:27:41 3.770u 0.229s 0:04.32 92.3% 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 09:27:41 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 = 2728 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: 1.719585 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): -79.77600 -31.94200 ymin,ymax (A): -34.74500 27.36300 zmin,zma (A): -51.51000 7.511000 x,y,z range (A): 47.83400 62.10800 59.02100 scale (grids/A): 1.719585 object centre (A): -55.85900 -3.691002 -21.99950 number of atom coordinates read : 2728 total number of charged atoms : 2584 net assigned charge : 1.000018 assigned positive charge : 404.1206 centred at (gu) : 87.92271 86.87735 84.74685 assigned negative charge : -403.1215 centred at (gu) : 87.97414 87.56399 84.96233 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66207 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26484 grid for indexing accessible points = 1.400000 m= 22004 mr = 43673 m= 2682 mr = 15280 m= 90 mr = 1345 m= 0 mr = 8 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.3400000 number of dielectric boundary points 30677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20008 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) : 0.5731950 object centre at (A) : -55.85900 -3.691002 -21.99950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5345300E-03 1.1258444E-03 midg,1,midg; midg,igrid,midg 1.1056546E-02 -2.0235697E-02 1,midg,midg; igrid,midg,midg 7.9816403E-03 2.8637059E-03 gauss-seidel spectral radius is 0.9983526 estimated iterations to convergence 196 setup time was (sec) 0.5800000 now iterating at: 09:27:42 rms-change max change #iterations 3.502473 172.0818 at 10iterations 1.509547 67.46802 at 20iterations 0.6518357 23.68774 at 30iterations 0.2830884 10.54165 at 40iterations 0.1223569 4.410362 at 50iterations 5.3191565E-02 2.000967 at 60iterations 2.3060137E-02 0.8467488 at 70iterations 1.0017364E-02 0.4402161 at 80iterations 4.3449365E-03 0.1458569 at 90iterations 1.8899220E-03 6.4989090E-02 at 100iterations 8.2454225E-04 2.8259277E-02 at 110iterations 3.5763587E-04 1.2046337E-02 at 120iterations finished qdiffx linear iterations at : 09:27:49 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 3.5763587E-04 1.2046337E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 09:27:50 8.121u 0.220s 0:08.66 96.3% 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 09:27:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 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: 2.579378 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): -79.77600 -31.94200 ymin,ymax (A): -34.74500 27.36300 zmin,zma (A): -51.51000 7.511000 x,y,z range (A): 47.83400 62.10800 59.02100 scale (grids/A): 2.579378 object centre (A): -55.85900 -3.691002 -21.99950 number of atom coordinates read : 2728 total number of charged atoms : 2584 net assigned charge : 1.000018 assigned positive charge : 404.1206 centred at (gu) : 86.88397 85.31586 82.12008 assigned negative charge : -403.1215 centred at (gu) : 86.96115 86.34599 82.44352 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 153186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26484 grid for indexing accessible points = 1.400000 m= 72899 mr = 106631 m= 23499 mr = 57620 m= 4381 mr = 17900 m= 365 mr = 2842 m= 10 mr = 173 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 385 time to turn everything in is 0.8300000 number of dielectric boundary points 69172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20662 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) : 1.719585 object centre at (A) : -55.85900 -3.691002 -21.99950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0284415E-02 -3.0179275E-02 midg,1,midg; midg,igrid,midg 0.2948401 -1.3880578E-02 1,midg,midg; igrid,midg,midg 0.1239569 2.8290249E-02 gauss-seidel spectral radius is 0.9991869 estimated iterations to convergence 277 setup time was (sec) 1.070000 now iterating at: 09:27:51 rms-change max change #iterations 8.783551 247.1434 at 10iterations 5.031848 118.0518 at 20iterations 2.856624 66.02105 at 30iterations 1.618044 35.96136 at 40iterations 0.9102359 18.75893 at 50iterations 0.5117355 12.63052 at 60iterations 0.2867830 5.965118 at 70iterations 0.1611898 3.424927 at 80iterations 9.0480171E-02 1.926510 at 90iterations 5.0599519E-02 1.136663 at 100iterations 2.8336655E-02 0.5468271 at 110iterations 1.5852252E-02 0.3239403 at 120iterations 8.8673774E-03 0.1892500 at 130iterations 4.9591037E-03 9.8983765E-02 at 140iterations 2.7734877E-03 6.2722206E-02 at 150iterations 1.5519442E-03 3.1351089E-02 at 160iterations 8.6747215E-04 1.7425537E-02 at 170iterations 4.8635472E-04 1.0173798E-02 at 180iterations finished qdiffx linear iterations at : 09:28:03 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 4.8635472E-04 1.0173798E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 09:28:03 13.253u 0.263s 0:13.78 98.0% 0+0k 0+0io 0pf+0w