Wed Dec 21 14:21:48 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+sph2.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 = amb2.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 Wed Dec 21 2011 at 14:21:50 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 0.6420893 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): -5.823000 34.78900 ymin,ymax (A): -3.567000 49.04100 zmin,zma (A): -24.38400 31.06000 x,y,z range (A): 40.61200 52.60800 55.44400 scale (grids/A): 0.6420893 object centre (A): 14.48300 22.73700 3.338000 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 291.0140 centred at (gu) : 90.83317 92.41131 90.19917 assigned negative charge : -288.3333 centred at (gu) : 90.95461 92.56429 90.13553 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5636 nv = 96 ne = 84 npr = 39735 no. pairs analyzed = 39735 no. exposed pairs = 2476 no. arc points = 17405 no. surface atoms = 838 nbur = 1127 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3165 m= 0 mr = 48 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2800000 number of dielectric boundary points 2740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1691 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6519 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1635517E-09 1.0799909E-08 midg,1,midg; midg,igrid,midg 1.0977801E-08 -1.6477806E-08 1,midg,midg; igrid,midg,midg 1.2979853E-08 -7.9567908E-09 gauss-seidel spectral radius is 0.9873784 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 14:21:51 rms-change max change #iterations 0.1290040 19.48864 at 10iterations 1.2986749E-02 1.775594 at 20iterations 1.2758450E-03 0.1933479 at 30iterations 1.2462320E-04 1.8930197E-02 at 40iterations 1.2472830E-05 1.9526482E-03 at 50iterations finished qdiffx linear iterations at : 14:21:55 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 1.2472830E-05 1.9526482E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 14:21:59 4.006u 0.273s 0:09.26 46.1% 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 Wed Dec 21 2011 at 14:22:01 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 1.926268 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): -5.823000 34.78900 ymin,ymax (A): -3.567000 49.04100 zmin,zma (A): -24.38400 31.06000 x,y,z range (A): 40.61200 52.60800 55.44400 scale (grids/A): 1.926268 object centre (A): 14.48300 22.73700 3.338000 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 291.0140 centred at (gu) : 92.49951 97.23392 90.59734 assigned negative charge : -288.3333 centred at (gu) : 92.86393 97.69299 90.40675 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17405 grid for indexing accessible points = 1.400000 m= 23043 mr = 41686 m= 3965 mr = 17737 m= 212 mr = 2655 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2574 time to turn everything in is 0.5600000 number of dielectric boundary points 25184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 14458 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) : 0.6420893 object centre at (A) : 14.48300 22.73700 3.338000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1185431E-02 1.1381344E-02 midg,1,midg; midg,igrid,midg 3.3634424E-02 -1.3721397E-02 1,midg,midg; igrid,midg,midg 8.4279189E-03 -5.5433218E-03 gauss-seidel spectral radius is 0.9985893 estimated iterations to convergence 211 setup time was (sec) 0.8400000 now iterating at: 14:22:03 rms-change max change #iterations 3.672492 187.5811 at 10iterations 1.695756 63.09943 at 20iterations 0.7874327 26.87750 at 30iterations 0.3644888 13.09998 at 40iterations 0.1674274 5.595160 at 50iterations 7.7567622E-02 2.586956 at 60iterations 3.5809621E-02 1.218253 at 70iterations 1.6578330E-02 0.5589180 at 80iterations 7.6576076E-03 0.2853817 at 90iterations 3.5547947E-03 0.1454039 at 100iterations 1.6407163E-03 5.9358954E-02 at 110iterations 7.5871625E-04 2.5421143E-02 at 120iterations finished qdiffx linear iterations at : 14:22:11 total time elapsed so far: 9.020000 # loops : 120 mean,max change (kT/e) : 7.5871625E-04 2.5421143E-02 energy calculations done at 9.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.180000 DelPhi exited at 14:22:15 9.183u 0.332s 0:13.75 69.1% 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 Wed Dec 21 2011 at 14:22:15 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 2.889402 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): -5.823000 34.78900 ymin,ymax (A): -3.567000 49.04100 zmin,zma (A): -24.38400 31.06000 x,y,z range (A): 40.61200 52.60800 55.44400 scale (grids/A): 2.889402 object centre (A): 14.48300 22.73700 3.338000 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681006 assigned positive charge : 291.0140 centred at (gu) : 93.74910 100.8511 90.89599 assigned negative charge : -288.3333 centred at (gu) : 94.29594 101.5395 90.61034 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 138795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17405 grid for indexing accessible points = 1.400000 m= 72848 mr = 100532 m= 28569 mr = 60794 m= 7181 mr = 23887 m= 985 mr = 5638 m= 64 mr = 705 m= 0 mr = 33 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 8409 time to turn everything in is 1.420000 number of dielectric boundary points 56853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 14655 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) : 1.926268 object centre at (A) : 14.48300 22.73700 3.338000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9729459 5.2779410E-03 midg,1,midg; midg,igrid,midg 0.3583838 -0.1539219 1,midg,midg; igrid,midg,midg 5.3888075E-02 -3.6866605E-02 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.740000 now iterating at: 14:22:17 rms-change max change #iterations 8.672545 539.5657 at 10iterations 4.987388 147.7731 at 20iterations 2.839955 79.17762 at 30iterations 1.618570 41.26884 at 40iterations 0.9255849 21.62102 at 50iterations 0.5266884 11.26106 at 60iterations 0.2999165 6.197399 at 70iterations 0.1702271 3.774033 at 80iterations 9.6885979E-02 2.134155 at 90iterations 5.5099998E-02 1.133062 at 100iterations 3.1319920E-02 0.6402980 at 110iterations 1.7773867E-02 0.3659487 at 120iterations 1.0087801E-02 0.2075341 at 130iterations 5.7381736E-03 0.1148796 at 140iterations 3.2601487E-03 6.4188004E-02 at 150iterations 1.8482477E-03 3.7752151E-02 at 160iterations 1.0489778E-03 2.1948814E-02 at 170iterations 5.9568940E-04 1.1372089E-02 at 180iterations finished qdiffx linear iterations at : 14:22:31 total time elapsed so far: 15.15000 # loops : 180 mean,max change (kT/e) : 5.9568940E-04 1.1372089E-02 energy calculations done at 15.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.32000 DelPhi exited at 14:22:34 15.323u 0.355s 0:19.52 80.2% 0+0k 0+0io 0pf+0w