Sat Oct 8 15:47:03 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 Sat Oct 8 2011 at 15:47:03 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.6479442 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): -45.36600 2.639000 ymin,ymax (A): 3.740000 50.00500 zmin,zma (A): -18.54700 36.39600 x,y,z range (A): 48.00500 46.26500 54.94300 scale (grids/A): 0.6479442 object centre (A): -21.36350 26.87250 8.924500 number of atom coordinates read : 2452 total number of charged atoms : 2381 net assigned charge : 1.806003 assigned positive charge : 369.2328 centred at (gu) : 88.69872 91.10601 90.62405 assigned negative charge : -367.4277 centred at (gu) : 88.64729 90.93351 90.72608 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7132 nv = 96 ne = 84 npr = 48207 no. pairs analyzed = 48207 no. exposed pairs = 3109 no. arc points = 21421 no. surface atoms = 1058 nbur = 1394 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 440 mr = 4014 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2099 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4869078E-08 -1.2441465E-08 midg,1,midg; midg,igrid,midg -1.6320095E-08 3.3393832E-08 1,midg,midg; igrid,midg,midg -5.1510773E-09 7.7538811E-09 gauss-seidel spectral radius is 0.9876477 estimated iterations to convergence 74 setup time was (sec) 0.4800000 now iterating at: 15:47:03 rms-change max change #iterations 0.1487020 25.12652 at 10iterations 1.5222392E-02 2.040443 at 20iterations 1.5883461E-03 0.2131481 at 30iterations 1.8479575E-04 2.7307510E-02 at 40iterations 3.0156059E-05 4.1997433E-03 at 50iterations finished qdiffx linear iterations at : 15:47:06 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 3.0156059E-05 4.1997433E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 15:47:06 3.126u 0.177s 0:03.59 91.6% 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 Sat Oct 8 2011 at 15:47:06 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.943833 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): -45.36600 2.639000 ymin,ymax (A): 3.740000 50.00500 zmin,zma (A): -18.54700 36.39600 x,y,z range (A): 48.00500 46.26500 54.94300 scale (grids/A): 1.943833 object centre (A): -21.36350 26.87250 8.924500 number of atom coordinates read : 2452 total number of charged atoms : 2381 net assigned charge : 1.806003 assigned positive charge : 369.2328 centred at (gu) : 86.09563 93.31739 91.87160 assigned negative charge : -367.4277 centred at (gu) : 85.94177 92.80045 92.17820 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21421 grid for indexing accessible points = 1.400000 m= 28880 mr = 53851 m= 5249 mr = 21620 m= 329 mr = 3601 m= 6 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 742 time to turn everything in is 0.5400000 number of dielectric boundary points 31958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18781 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) : 0.6479442 object centre at (A) : -21.36350 26.87250 8.924500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9207017E-02 -1.8495832E-02 midg,1,midg; midg,igrid,midg -7.1783317E-03 2.9394377E-02 1,midg,midg; igrid,midg,midg -5.6365423E-02 1.9465571E-03 gauss-seidel spectral radius is 0.9986765 estimated iterations to convergence 218 setup time was (sec) 0.8100000 now iterating at: 15:47:07 rms-change max change #iterations 4.333510 177.6268 at 10iterations 2.053599 88.11807 at 20iterations 0.9737511 30.98222 at 30iterations 0.4638303 16.32608 at 40iterations 0.2198825 7.265152 at 50iterations 0.1045745 3.193769 at 60iterations 4.9626943E-02 1.480759 at 70iterations 2.3529384E-02 0.8072538 at 80iterations 1.1176550E-02 0.3528061 at 90iterations 5.3052199E-03 0.1721611 at 100iterations 2.5207270E-03 8.0039978E-02 at 110iterations 1.2011003E-03 3.4867406E-02 at 120iterations finished qdiffx linear iterations at : 15:47:13 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.2011003E-03 3.4867406E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 15:47:14 6.999u 0.212s 0:07.49 96.1% 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 Sat Oct 8 2011 at 15:47:14 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.915749 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): -45.36600 2.639000 ymin,ymax (A): 3.740000 50.00500 zmin,zma (A): -18.54700 36.39600 x,y,z range (A): 48.00500 46.26500 54.94300 scale (grids/A): 2.915749 object centre (A): -21.36350 26.87250 8.924500 number of atom coordinates read : 2452 total number of charged atoms : 2381 net assigned charge : 1.806003 assigned positive charge : 369.2328 centred at (gu) : 84.14336 94.97604 92.80735 assigned negative charge : -367.4277 centred at (gu) : 83.91261 94.20059 93.26724 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 177398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21421 grid for indexing accessible points = 1.400000 m= 91957 mr = 130342 m= 35720 mr = 75841 m= 9914 mr = 29312 m= 1513 mr = 7892 m= 121 mr = 1095 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 2654 time to turn everything in is 1.380000 number of dielectric boundary points 72068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19048 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) : 1.943833 object centre at (A) : -21.36350 26.87250 8.924500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3086576 -0.2465352 midg,1,midg; midg,igrid,midg -0.1012229 0.2199768 1,midg,midg; igrid,midg,midg -0.6972286 3.3249613E-02 gauss-seidel spectral radius is 0.9992725 estimated iterations to convergence 293 setup time was (sec) 1.660000 now iterating at: 15:47:16 rms-change max change #iterations 10.13684 500.7413 at 10iterations 5.977531 154.1432 at 20iterations 3.513306 88.16289 at 30iterations 2.058649 40.61102 at 40iterations 1.204707 22.20444 at 50iterations 0.7007599 13.01513 at 60iterations 0.4080833 7.403179 at 70iterations 0.2367412 4.504745 at 80iterations 0.1373453 2.540932 at 90iterations 7.9724684E-02 1.565531 at 100iterations 4.6261255E-02 0.8898935 at 110iterations 2.6753381E-02 0.5128250 at 120iterations 1.5487194E-02 0.2954330 at 130iterations 8.9771999E-03 0.1641293 at 140iterations 5.1917871E-03 8.7773323E-02 at 150iterations 3.0030259E-03 5.0667763E-02 at 160iterations 1.7509030E-03 3.6804199E-02 at 170iterations 1.0241083E-03 1.8155575E-02 at 180iterations finished qdiffx linear iterations at : 15:47:25 total time elapsed so far: 11.39000 # loops : 180 mean,max change (kT/e) : 1.0241083E-03 1.8155575E-02 energy calculations done at 11.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.57000 DelPhi exited at 15:47:26 11.571u 0.237s 0:12.09 97.6% 0+0k 0+0io 0pf+0w