Sun Oct 9 14:12:50 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 14:12:50 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 = 2466 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6374674 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 0.6374674 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2330 net assigned charge : 8.500018 assigned positive charge : 370.3150 centred at (gu) : 89.37457 90.98524 90.14650 assigned negative charge : -361.8158 centred at (gu) : 89.31995 90.90057 90.00490 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6710 nv = 96 ne = 84 npr = 50355 no. pairs analyzed = 50355 no. exposed pairs = 3030 no. arc points = 21178 no. surface atoms = 1023 nbur = 1443 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3671 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0357008E-09 2.6377235E-08 midg,1,midg; midg,igrid,midg 2.3372686E-09 2.4599590E-08 1,midg,midg; igrid,midg,midg 6.6220522E-09 1.4844888E-08 gauss-seidel spectral radius is 0.9872384 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 14:12:50 rms-change max change #iterations 0.1377989 20.34429 at 10iterations 1.3447053E-02 1.890604 at 20iterations 1.3032882E-03 0.2042923 at 30iterations 1.3151283E-04 1.7759323E-02 at 40iterations 1.4750065E-05 2.0599365E-03 at 50iterations finished qdiffx linear iterations at : 14:12:53 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.4750065E-05 2.0599365E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 14:12:53 3.099u 0.145s 0:03.53 91.5% 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 14:12:53 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 = 2466 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.912402 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 1.912402 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2330 net assigned charge : 8.500018 assigned positive charge : 370.3150 centred at (gu) : 88.12311 92.95525 90.43904 assigned negative charge : -361.8158 centred at (gu) : 87.95977 92.70158 90.01444 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21178 grid for indexing accessible points = 1.400000 m= 25599 mr = 50429 m= 3563 mr = 18348 m= 175 mr = 1942 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 357 time to turn everything in is 0.4900000 number of dielectric boundary points 31195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 18310 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) : 0.6374674 object centre at (A) : 20.66450 33.49400 37.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3149391E-02 6.4733244E-02 midg,1,midg; midg,igrid,midg -1.6418308E-02 9.1314400E-03 1,midg,midg; igrid,midg,midg 3.2027513E-02 4.0597677E-02 gauss-seidel spectral radius is 0.9986348 estimated iterations to convergence 214 setup time was (sec) 0.7500000 now iterating at: 14:12:54 rms-change max change #iterations 4.108079 171.0268 at 10iterations 1.917412 71.71638 at 20iterations 0.8972615 30.50382 at 30iterations 0.4199390 15.05783 at 40iterations 0.1972454 6.929121 at 50iterations 9.2041336E-02 3.001245 at 60iterations 4.3261528E-02 1.355692 at 70iterations 2.0177128E-02 0.6277390 at 80iterations 9.4880145E-03 0.3132291 at 90iterations 4.4434909E-03 0.1349754 at 100iterations 2.0854550E-03 7.0638657E-02 at 110iterations 9.7699510E-04 3.2005310E-02 at 120iterations finished qdiffx linear iterations at : 14:13:01 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 9.7699510E-04 3.2005310E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 14:13:01 7.461u 0.170s 0:07.92 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 14:13:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.868603 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 2.868603 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2330 net assigned charge : 8.500018 assigned positive charge : 370.3150 centred at (gu) : 87.18443 94.43269 90.65846 assigned negative charge : -361.8158 centred at (gu) : 86.93966 94.05229 90.02170 start vw surface at 0.2000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21178 grid for indexing accessible points = 1.400000 m= 83818 mr = 122530 m= 28621 mr = 67900 m= 6143 mr = 22212 m= 727 mr = 4230 m= 38 mr = 355 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 1182 time to turn everything in is 1.310000 number of dielectric boundary points 70158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 18634 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) : 1.912402 object centre at (A) : 20.66450 33.49400 37.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6639197E-02 0.5876021 midg,1,midg; midg,igrid,midg -0.1452181 7.1567729E-02 1,midg,midg; igrid,midg,midg 0.3336314 0.4744837 gauss-seidel spectral radius is 0.9992554 estimated iterations to convergence 289 setup time was (sec) 1.580000 now iterating at: 14:13:03 rms-change max change #iterations 9.739892 513.1779 at 10iterations 5.708138 175.5212 at 20iterations 3.333391 65.39333 at 30iterations 1.942269 36.01022 at 40iterations 1.124984 20.99972 at 50iterations 0.6518830 11.96736 at 60iterations 0.3763443 7.805311 at 70iterations 0.2170192 4.138885 at 80iterations 0.1254622 2.261887 at 90iterations 7.2150111E-02 1.336178 at 100iterations 4.1572198E-02 0.7818127 at 110iterations 2.3862636E-02 0.4624596 at 120iterations 1.3730128E-02 0.2856321 at 130iterations 7.8809084E-03 0.1582489 at 140iterations 4.5307316E-03 9.2346668E-02 at 150iterations 2.6006321E-03 4.8751831E-02 at 160iterations 1.4944348E-03 3.0704021E-02 at 170iterations 8.5820252E-04 1.6420364E-02 at 180iterations finished qdiffx linear iterations at : 14:13:12 total time elapsed so far: 10.94000 # loops : 180 mean,max change (kT/e) : 8.5820252E-04 1.6420364E-02 energy calculations done at 10.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 14:13:13 11.115u 0.166s 0:11.59 97.2% 0+0k 0+0io 0pf+0w