Mon Oct 10 16:05:23 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+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 Mon Oct 10 2011 at 16:05:23 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 848 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5491200 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): -20.14300 31.30200 ymin,ymax (A): -34.26000 29.61600 zmin,zma (A): -29.26200 35.56900 x,y,z range (A): 51.44500 63.87600 64.83100 scale (grids/A): 0.5491200 object centre (A): 5.579500 -2.322001 3.153501 number of atom coordinates read : 4352 total number of charged atoms : 4202 net assigned charge : 3.606015 assigned positive charge : 652.2239 centred at (gu) : 90.20441 90.24410 88.62516 assigned negative charge : -648.6213 centred at (gu) : 90.22936 90.27502 88.58214 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8492 nv = 96 ne = 84 npr = 88472 no. pairs analyzed = 88472 no. exposed pairs = 5264 no. arc points = 36044 no. surface atoms = 1772 nbur = 2580 mkacc time = 0.2400000 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= 366 mr = 4734 m= 0 mr = 25 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3636 ## 463 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 11188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0091693E-10 5.1980353E-10 midg,1,midg; midg,igrid,midg 5.6231048E-10 -8.1161376E-11 1,midg,midg; igrid,midg,midg 5.0648619E-10 -1.1347324E-11 gauss-seidel spectral radius is 0.9829990 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 16:05:24 rms-change max change #iterations 9.4819844E-02 14.18051 at 10iterations 6.6753486E-03 0.9380703 at 20iterations 6.4811890E-04 0.1118622 at 30iterations 1.6512547E-04 3.0906677E-02 at 40iterations 6.1174440E-05 9.6607208E-03 at 50iterations finished qdiffx linear iterations at : 16:05:28 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 6.1174440E-05 9.6607208E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 16:05:28 4.643u 0.398s 0:05.47 91.9% 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 Mon Oct 10 2011 at 16:05:28 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 848 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.647360 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): -20.14300 31.30200 ymin,ymax (A): -34.26000 29.61600 zmin,zma (A): -29.26200 35.56900 x,y,z range (A): 51.44500 63.87600 64.83100 scale (grids/A): 1.647360 object centre (A): 5.579500 -2.322001 3.153501 number of atom coordinates read : 4352 total number of charged atoms : 4202 net assigned charge : 3.606015 assigned positive charge : 652.2239 centred at (gu) : 90.61217 90.73051 85.87375 assigned negative charge : -648.6213 centred at (gu) : 90.68732 90.82468 85.74599 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 95320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36044 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 31144 mr = 67897 m= 3367 mr = 21920 m= 100 mr = 1776 m= 0 mr = 9 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 183 time to turn everything in is 0.7700000 number of dielectric boundary points 38329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 354 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 32201 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) : 0.5491200 object centre at (A) : 5.579500 -2.322001 3.153501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3092398E-02 -5.4264786E-03 midg,1,midg; midg,igrid,midg 1.9556118E-02 1.6680485E-02 1,midg,midg; igrid,midg,midg -5.7287031E-04 7.5990660E-04 gauss-seidel spectral radius is 0.9983553 estimated iterations to convergence 196 setup time was (sec) 1.080000 now iterating at: 16:05:30 rms-change max change #iterations 4.208865 163.6100 at 10iterations 1.828675 64.69366 at 20iterations 0.7949701 26.80906 at 30iterations 0.3464869 10.89534 at 40iterations 0.1507735 4.858791 at 50iterations 6.5736130E-02 2.024189 at 60iterations 2.8770847E-02 0.8784914 at 70iterations 1.2551412E-02 0.3618088 at 80iterations 5.4965215E-03 0.1717072 at 90iterations 2.4180436E-03 7.1363449E-02 at 100iterations 1.0773146E-03 3.2997131E-02 at 110iterations 4.9404200E-04 1.3931274E-02 at 120iterations finished qdiffx linear iterations at : 16:05:40 total time elapsed so far: 10.93000 # loops : 120 mean,max change (kT/e) : 4.9404200E-04 1.3931274E-02 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 16:05:40 11.100u 0.429s 0:11.86 97.1% 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 Mon Oct 10 2011 at 16:05:40 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4352 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 848 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.471040 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): -20.14300 31.30200 ymin,ymax (A): -34.26000 29.61600 zmin,zma (A): -29.26200 35.56900 x,y,z range (A): 51.44500 63.87600 64.83100 scale (grids/A): 2.471040 object centre (A): 5.579500 -2.322001 3.153501 number of atom coordinates read : 4352 total number of charged atoms : 4202 net assigned charge : 3.606015 assigned positive charge : 652.2239 centred at (gu) : 90.91772 91.09554 83.81026 assigned negative charge : -648.6213 centred at (gu) : 91.03083 91.23689 83.61866 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 221889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36044 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106698 mr = 166010 m= 31595 mr = 85630 m= 5370 mr = 24167 m= 403 mr = 3602 m= 8 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 566 time to turn everything in is 1.960000 number of dielectric boundary points 86360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 33589 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) : 1.647360 object centre at (A) : 5.579500 -2.322001 3.153501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5106040 -0.1232589 midg,1,midg; midg,igrid,midg 0.2821029 0.3403276 1,midg,midg; igrid,midg,midg 1.2643364E-02 1.6168594E-02 gauss-seidel spectral radius is 0.9992206 estimated iterations to convergence 283 setup time was (sec) 2.300000 now iterating at: 16:05:43 rms-change max change #iterations 10.83785 353.3375 at 10iterations 6.322984 133.8768 at 20iterations 3.675381 75.91080 at 30iterations 2.122494 40.11256 at 40iterations 1.221097 21.11604 at 50iterations 0.7018194 13.12545 at 60iterations 0.4018093 7.094994 at 70iterations 0.2294992 3.822960 at 80iterations 0.1312630 2.199225 at 90iterations 7.4824177E-02 1.220369 at 100iterations 4.2540900E-02 0.7433548 at 110iterations 2.4231588E-02 0.4127703 at 120iterations 1.3800958E-02 0.2397614 at 130iterations 7.8700930E-03 0.1353054 at 140iterations 4.4920673E-03 7.9857826E-02 at 150iterations 2.5713374E-03 4.5043945E-02 at 160iterations 1.4897515E-03 2.6844025E-02 at 170iterations 8.7653042E-04 1.4411926E-02 at 180iterations finished qdiffx linear iterations at : 16:06:00 total time elapsed so far: 19.09000 # loops : 180 mean,max change (kT/e) : 8.7653042E-04 1.4411926E-02 energy calculations done at 19.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.26000 DelPhi exited at 16:06:00 19.268u 0.463s 0:20.03 98.4% 0+0k 0+0io 0pf+0w