Tue Nov 22 14:10:14 PST 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 Tue Nov 22 2011 at 14:10:20 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.5525376 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): -35.35300 11.72500 ymin,ymax (A): 0.4230000 42.76200 zmin,zma (A): -3.419000 61.01100 x,y,z range (A): 47.07800 42.33900 64.43000 scale (grids/A): 0.5525376 object centre (A): -11.81400 21.59250 28.79600 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.03848 89.34178 89.43828 assigned negative charge : -286.4003 centred at (gu) : 89.96136 89.47027 89.44044 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 3983 nv = 96 ne = 84 npr = 40375 no. pairs analyzed = 40375 no. exposed pairs = 2456 no. arc points = 17327 no. surface atoms = 833 nbur = 1137 mkacc time = 8.0000006E-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 = 1.568000 m= 149 mr = 2098 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1823 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8326871E-10 1.9630102E-10 midg,1,midg; midg,igrid,midg 1.0893501E-09 -4.0304968E-10 1,midg,midg; igrid,midg,midg -1.8703050E-10 6.5888289E-10 gauss-seidel spectral radius is 0.9830282 estimated iterations to convergence 63 setup time was (sec) 0.4200000 now iterating at: 14:10:24 rms-change max change #iterations 5.9497181E-02 12.97863 at 10iterations 4.0277387E-03 0.7871733 at 20iterations 2.7541310E-04 5.8132172E-02 at 30iterations 1.8971034E-05 3.9062500E-03 at 40iterations 1.3117480E-06 2.6941299E-04 at 50iterations finished qdiffx linear iterations at : 14:10:32 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 1.3117480E-06 2.6941299E-04 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 14:10:33 3.059u 0.156s 0:14.10 22.6% 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 Tue Nov 22 2011 at 14:10:36 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.657613 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): -35.35300 11.72500 ymin,ymax (A): 0.4230000 42.76200 zmin,zma (A): -3.419000 61.01100 x,y,z range (A): 47.07800 42.33900 64.43000 scale (grids/A): 1.657613 object centre (A): -11.81400 21.59250 28.79600 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.11532 88.02516 88.31468 assigned negative charge : -286.4003 centred at (gu) : 89.88425 88.41097 88.32162 start vw surface at 0.1100000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 43478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17327 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 14026 mr = 29224 m= 1507 mr = 10157 m= 37 mr = 821 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 452 time to turn everything in is 0.3200000 number of dielectric boundary points 18846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 14149 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) : 0.5525376 object centre at (A) : -11.81400 21.59250 28.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9619983E-02 1.3978536E-02 midg,1,midg; midg,igrid,midg 2.2550263E-03 -3.8011514E-03 1,midg,midg; igrid,midg,midg -1.4490621E-03 3.9440271E-04 gauss-seidel spectral radius is 0.9981166 estimated iterations to convergence 183 setup time was (sec) 0.5800000 now iterating at: 14:10:40 rms-change max change #iterations 2.695441 158.8014 at 10iterations 1.099337 50.36823 at 20iterations 0.4526152 20.83385 at 30iterations 0.1852511 7.531172 at 40iterations 7.6072492E-02 3.608448 at 50iterations 3.1084331E-02 1.498952 at 60iterations 1.2667184E-02 0.5569992 at 70iterations 5.2120518E-03 0.2239990 at 80iterations 2.1461309E-03 9.6342087E-02 at 90iterations 8.8097405E-04 3.5972595E-02 at 100iterations 3.6138904E-04 1.5848160E-02 at 110iterations 1.4841717E-04 6.8321228E-03 at 120iterations finished qdiffx linear iterations at : 14:10:58 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 1.4841717E-04 6.8321228E-03 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 14:11:00 6.809u 0.183s 0:25.10 27.8% 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 Tue Nov 22 2011 at 14:11:02 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.486419 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): -35.35300 11.72500 ymin,ymax (A): 0.4230000 42.76200 zmin,zma (A): -3.419000 61.01100 x,y,z range (A): 47.07800 42.33900 64.43000 scale (grids/A): 2.486419 object centre (A): -11.81400 21.59250 28.79600 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.17306 87.03775 87.47202 assigned negative charge : -286.4003 centred at (gu) : 89.82643 87.61651 87.48254 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 100746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17327 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 47909 mr = 71235 m= 14558 mr = 38779 m= 2501 mr = 11599 m= 148 mr = 1690 m= 4 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1524 time to turn everything in is 0.7500000 number of dielectric boundary points 42492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14694 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) : 1.657613 object centre at (A) : -11.81400 21.59250 28.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2120741 0.1309018 midg,1,midg; midg,igrid,midg 3.4156879E-03 -6.7496322E-02 1,midg,midg; igrid,midg,midg -3.4301486E-02 -1.7517062E-02 gauss-seidel spectral radius is 0.9990792 estimated iterations to convergence 260 setup time was (sec) 1.040000 now iterating at: 14:11:08 rms-change max change #iterations 6.866897 283.8273 at 10iterations 3.739227 111.8429 at 20iterations 2.026721 52.76443 at 30iterations 1.091857 28.35818 at 40iterations 0.5899451 14.85811 at 50iterations 0.3185373 7.574374 at 60iterations 0.1717694 4.573051 at 70iterations 9.2139840E-02 2.306861 at 80iterations 4.9666986E-02 1.230991 at 90iterations 2.6704783E-02 0.6537781 at 100iterations 1.4342754E-02 0.3521976 at 110iterations 7.7119465E-03 0.2123489 at 120iterations 4.1447924E-03 0.1092663 at 130iterations 2.2320596E-03 5.3742409E-02 at 140iterations 1.1983569E-03 3.2165527E-02 at 150iterations 6.4485997E-04 1.5319824E-02 at 160iterations 3.4515042E-04 9.7045898E-03 at 170iterations 1.8585578E-04 4.3950081E-03 at 180iterations finished qdiffx linear iterations at : 14:11:27 total time elapsed so far: 10.47000 # loops : 180 mean,max change (kT/e) : 1.8585578E-04 4.3950081E-03 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 14:11:29 10.642u 0.169s 0:27.51 39.2% 0+0k 0+0io 0pf+0w