Wed Feb 15 08:55:22 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:22 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 = 3451 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: 0.6428894 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 0.6428894 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 529.5694 centred at (gu) : 89.40562 90.85578 89.24240 assigned negative charge : -526.5706 centred at (gu) : 89.42934 90.81654 89.31229 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9325 nv = 96 ne = 84 npr = 72485 no. pairs analyzed = 72485 no. exposed pairs = 3905 no. arc points = 26688 no. surface atoms = 1312 nbur = 2139 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 503 mr = 5479 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.4100000 number of dielectric boundary points 4295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2644 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 11447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9311537E-08 -6.3238943E-09 midg,1,midg; midg,igrid,midg -1.7794454E-09 1.3480672E-08 1,midg,midg; igrid,midg,midg 9.7464863E-09 4.5316337E-10 gauss-seidel spectral radius is 0.9875260 estimated iterations to convergence 73 setup time was (sec) 0.6400000 now iterating at: 08:55:23 rms-change max change #iterations 0.1753032 22.23805 at 10iterations 1.8151969E-02 2.313008 at 20iterations 2.2108816E-03 0.2600441 at 30iterations 6.1426300E-04 8.9540482E-02 at 40iterations 2.7872861E-04 3.9352417E-02 at 50iterations finished qdiffx linear iterations at : 08:55:26 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.7872861E-04 3.9352417E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 08:55:26 3.487u 0.160s 0:04.16 87.5% 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 Wed Feb 15 2012 at 08:55:26 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 = 3451 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: 1.928668 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 1.928668 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 529.5694 centred at (gu) : 88.21597 92.56623 87.72642 assigned negative charge : -526.5706 centred at (gu) : 88.28757 92.44934 87.93651 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 100403 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26688 grid for indexing accessible points = 1.400000 m= 39450 mr = 72839 m= 6777 mr = 30063 m= 430 mr = 4320 m= 8 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 2203 time to turn everything in is 0.7400000 number of dielectric boundary points 39697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 26067 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) : 0.6428894 object centre at (A) : 37.49150 -15.45050 58.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9624494E-02 -6.3170195E-03 midg,1,midg; midg,igrid,midg -7.1529159E-03 2.6636042E-02 1,midg,midg; igrid,midg,midg 1.5455045E-02 4.3484699E-02 gauss-seidel spectral radius is 0.9987331 estimated iterations to convergence 223 setup time was (sec) 1.040000 now iterating at: 08:55:28 rms-change max change #iterations 5.164255 207.5291 at 10iterations 2.497674 67.38225 at 20iterations 1.211121 32.95000 at 30iterations 0.5847554 15.60742 at 40iterations 0.2830870 8.466837 at 50iterations 0.1368663 3.957905 at 60iterations 6.6298135E-02 1.858620 at 70iterations 3.2129522E-02 1.003841 at 80iterations 1.5594096E-02 0.4227655 at 90iterations 7.6628830E-03 0.2002754 at 100iterations 3.8362942E-03 0.1225624 at 110iterations 2.0048181E-03 5.3882599E-02 at 120iterations finished qdiffx linear iterations at : 08:55:35 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 2.0048181E-03 5.3882599E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.420000 DelPhi exited at 08:55:35 8.428u 0.171s 0:09.05 94.9% 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 Wed Feb 15 2012 at 08:55:35 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 = 3451 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: 2.893002 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 2.893002 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 529.5694 centred at (gu) : 87.32381 93.84901 86.58964 assigned negative charge : -526.5706 centred at (gu) : 87.43120 93.67384 86.90479 start vw surface at 0.2100000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 231864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26688 grid for indexing accessible points = 1.400000 m= 125481 mr = 175330 m= 48607 mr = 104880 m= 12600 mr = 39747 m= 1896 mr = 9575 m= 126 mr = 1206 m= 0 mr = 59 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 7344 time to turn everything in is 1.950000 number of dielectric boundary points 89777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 26424 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) : 1.928668 object centre at (A) : 37.49150 -15.45050 58.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3986661 0.1789347 midg,1,midg; midg,igrid,midg -5.8122214E-02 0.3126040 1,midg,midg; igrid,midg,midg 0.2233182 0.5467082 gauss-seidel spectral radius is 0.9992938 estimated iterations to convergence 297 setup time was (sec) 2.260000 now iterating at: 08:55:39 rms-change max change #iterations 11.98847 516.5310 at 10iterations 7.165045 146.5759 at 20iterations 4.263796 100.1427 at 30iterations 2.517690 47.58479 at 40iterations 1.489872 27.20385 at 50iterations 0.8764077 16.33794 at 60iterations 0.5156919 8.730637 at 70iterations 0.3021468 5.202067 at 80iterations 0.1772894 3.041121 at 90iterations 0.1040519 1.707298 at 100iterations 6.0926307E-02 0.9542627 at 110iterations 3.5642583E-02 0.5636587 at 120iterations 2.0871390E-02 0.3463278 at 130iterations 1.2209272E-02 0.1802330 at 140iterations 7.1621635E-03 0.1116943 at 150iterations 4.2049992E-03 6.3510895E-02 at 160iterations 2.4855672E-03 4.1069031E-02 at 170iterations 1.4881790E-03 2.4917603E-02 at 180iterations finished qdiffx linear iterations at : 08:55:53 total time elapsed so far: 16.15000 # loops : 180 mean,max change (kT/e) : 1.4881790E-03 2.4917603E-02 energy calculations done at 16.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.33000 DelPhi exited at 08:55:54 16.332u 0.212s 0:18.09 91.4% 0+0k 0+0io 0pf+0w