Sat Oct 8 16:43:17 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 16:43:18 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4598 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5477345 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): 16.82000 78.78500 ymin,ymax (A): 118.8150 183.8100 zmin,zma (A): -1.776000 59.49400 x,y,z range (A): 61.96500 64.99500 61.27000 scale (grids/A): 0.5477345 object centre (A): 47.80250 151.3125 28.85900 number of atom coordinates read : 4598 total number of charged atoms : 4392 net assigned charge : 2.906037 assigned positive charge : 701.5328 centred at (gu) : 91.72359 89.26575 87.23451 assigned negative charge : -698.6301 centred at (gu) : 91.68558 89.17866 87.24786 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8770 nv = 96 ne = 84 npr = 93852 no. pairs analyzed = 93852 no. exposed pairs = 5461 no. arc points = 37787 no. surface atoms = 1835 nbur = 2763 mkacc time = 0.2000000 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= 391 mr = 4745 m= 0 mr = 37 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.4300000 number of dielectric boundary points 4379 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3893 ## 503 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 11698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6204159E-10 2.3202947E-11 midg,1,midg; midg,igrid,midg -9.4174823E-10 9.4469643E-10 1,midg,midg; igrid,midg,midg -1.4939169E-10 9.2663960E-10 gauss-seidel spectral radius is 0.9829321 estimated iterations to convergence 63 setup time was (sec) 0.6700000 now iterating at: 16:43:18 rms-change max change #iterations 9.3968637E-02 12.18376 at 10iterations 6.7115496E-03 1.092548 at 20iterations 6.5058062E-04 0.1037674 at 30iterations 1.4900818E-04 2.2397995E-02 at 40iterations 4.5722267E-05 7.2622299E-03 at 50iterations finished qdiffx linear iterations at : 16:43:21 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 4.5722267E-05 7.2622299E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 16:43:22 3.530u 0.235s 0:04.19 89.7% 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 16:43:22 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4598 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.643203 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): 16.82000 78.78500 ymin,ymax (A): 118.8150 183.8100 zmin,zma (A): -1.776000 59.49400 x,y,z range (A): 61.96500 64.99500 61.27000 scale (grids/A): 1.643203 object centre (A): 47.80250 151.3125 28.85900 number of atom coordinates read : 4598 total number of charged atoms : 4392 net assigned charge : 2.906037 assigned positive charge : 701.5328 centred at (gu) : 95.16953 87.79640 81.70234 assigned negative charge : -698.6301 centred at (gu) : 95.05672 87.53559 81.74329 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 98440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37787 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30758 mr = 69106 m= 3597 mr = 21436 m= 101 mr = 2003 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1668 time to turn everything in is 0.6900000 number of dielectric boundary points 40339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 436 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 33703 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) : 0.5477345 object centre at (A) : 47.80250 151.3125 28.85900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4503693E-03 9.1662509E-03 midg,1,midg; midg,igrid,midg 1.4860611E-02 3.3008847E-02 1,midg,midg; igrid,midg,midg -1.1164121E-02 -1.6263336E-02 gauss-seidel spectral radius is 0.9983575 estimated iterations to convergence 196 setup time was (sec) 1.010000 now iterating at: 16:43:23 rms-change max change #iterations 4.372341 248.4401 at 10iterations 1.902571 100.0314 at 20iterations 0.8251894 38.49582 at 30iterations 0.3600411 12.12402 at 40iterations 0.1568274 5.272823 at 50iterations 6.8269208E-02 2.184095 at 60iterations 2.9767277E-02 0.9265442 at 70iterations 1.2954357E-02 0.4162178 at 80iterations 5.6631742E-03 0.1700039 at 90iterations 2.4850720E-03 7.3219299E-02 at 100iterations 1.0873277E-03 3.1423569E-02 at 110iterations 4.7789715E-04 1.4440536E-02 at 120iterations finished qdiffx linear iterations at : 16:43:30 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 4.7789715E-04 1.4440536E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 16:43:31 8.198u 0.239s 0:08.79 95.7% 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 16:43:31 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4598 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.464805 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): 16.82000 78.78500 ymin,ymax (A): 118.8150 183.8100 zmin,zma (A): -1.776000 59.49400 x,y,z range (A): 61.96500 64.99500 61.27000 scale (grids/A): 2.464805 object centre (A): 47.80250 151.3125 28.85900 number of atom coordinates read : 4598 total number of charged atoms : 4392 net assigned charge : 2.906037 assigned positive charge : 701.5328 centred at (gu) : 97.75401 86.69439 77.55338 assigned negative charge : -698.6301 centred at (gu) : 97.58510 86.30313 77.61474 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 229471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37787 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106403 mr = 168961 m= 31238 mr = 85263 m= 5884 mr = 23648 m= 549 mr = 4181 m= 18 mr = 329 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 5523 time to turn everything in is 1.660000 number of dielectric boundary points 91181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 35098 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) : 1.643203 object centre at (A) : 47.80250 151.3125 28.85900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1225716E-03 0.1750571 midg,1,midg; midg,igrid,midg 0.2154451 0.5789143 1,midg,midg; igrid,midg,midg -0.1495080 -0.2694942 gauss-seidel spectral radius is 0.9992190 estimated iterations to convergence 282 setup time was (sec) 2.000000 now iterating at: 16:43:33 rms-change max change #iterations 11.17422 358.2628 at 10iterations 6.449665 135.9581 at 20iterations 3.702849 72.78449 at 30iterations 2.121829 37.96925 at 40iterations 1.210502 23.13306 at 50iterations 0.6900758 12.35400 at 60iterations 0.3925417 6.692432 at 70iterations 0.2224053 4.311233 at 80iterations 0.1263098 2.397532 at 90iterations 7.1549356E-02 1.197865 at 100iterations 4.0505994E-02 0.7127800 at 110iterations 2.3050426E-02 0.4321289 at 120iterations 1.3064394E-02 0.2377768 at 130iterations 7.3800967E-03 0.1274071 at 140iterations 4.1826195E-03 6.6810608E-02 at 150iterations 2.3705913E-03 3.8822174E-02 at 160iterations 1.3389981E-03 2.1658018E-02 at 170iterations 7.5945118E-04 1.4328003E-02 at 180iterations finished qdiffx linear iterations at : 16:43:44 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 7.5945118E-04 1.4328003E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.81000 DelPhi exited at 16:43:45 13.809u 0.268s 0:14.37 97.8% 0+0k 0+0io 0pf+0w