Sat Oct 8 15:53:03 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 15:53:03 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2350 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 0.6219535 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 0.6219535 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2350 total number of charged atoms : 2255 net assigned charge : 2.900002 assigned positive charge : 347.7231 centred at (gu) : 90.22926 88.34319 89.58801 assigned negative charge : -344.8238 centred at (gu) : 90.25862 88.44298 89.64618 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6080 nv = 96 ne = 84 npr = 47760 no. pairs analyzed = 47760 no. exposed pairs = 2885 no. arc points = 19999 no. surface atoms = 988 nbur = 1362 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3355 m= 0 mr = 36 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5127894E-09 -1.1771789E-09 midg,1,midg; midg,igrid,midg 1.2292262E-08 -2.6975440E-09 1,midg,midg; igrid,midg,midg 3.9695718E-09 5.3011062E-10 gauss-seidel spectral radius is 0.9865904 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 15:53:04 rms-change max change #iterations 0.1205173 19.48291 at 10iterations 1.1296560E-02 2.078196 at 20iterations 1.0895852E-03 0.1615276 at 30iterations 1.2413895E-04 2.3323059E-02 at 40iterations 2.2754779E-05 4.5118332E-03 at 50iterations finished qdiffx linear iterations at : 15:53:08 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 2.2754779E-05 4.5118332E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 15:53:08 4.241u 0.244s 0:04.74 94.5% 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 Sat Oct 8 2011 at 15:53:08 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2350 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.865861 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 1.865861 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2350 total number of charged atoms : 2255 net assigned charge : 2.900002 assigned positive charge : 347.7231 centred at (gu) : 90.68717 85.02870 88.76361 assigned negative charge : -344.8238 centred at (gu) : 90.77596 85.32861 88.93858 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66002 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19999 grid for indexing accessible points = 1.400000 m= 22814 mr = 46034 m= 3481 mr = 16720 m= 181 mr = 2219 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 0.5400000 number of dielectric boundary points 27437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17702 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) : 0.6219535 object centre at (A) : 21.54850 7.176000 10.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1981003E-02 -5.1431935E-03 midg,1,midg; midg,igrid,midg 2.0124545E-02 -2.1549889E-03 1,midg,midg; igrid,midg,midg 3.1643920E-03 -3.0623037E-02 gauss-seidel spectral radius is 0.9985506 estimated iterations to convergence 208 setup time was (sec) 0.8800000 now iterating at: 15:53:09 rms-change max change #iterations 3.848260 183.7491 at 10iterations 1.752749 72.52017 at 20iterations 0.8033141 29.82379 at 30iterations 0.3683957 12.57324 at 40iterations 0.1681713 6.028646 at 50iterations 7.7215575E-02 2.697698 at 60iterations 3.5276193E-02 1.209161 at 70iterations 1.6180903E-02 0.5527635 at 80iterations 7.4108019E-03 0.2590351 at 90iterations 3.4053896E-03 0.1109200 at 100iterations 1.5634215E-03 5.3547382E-02 at 110iterations 7.1958458E-04 2.3818970E-02 at 120iterations finished qdiffx linear iterations at : 15:53:18 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 7.1958458E-04 2.3818970E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 15:53:18 9.638u 0.279s 0:10.20 97.0% 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 15:53:18 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2350 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.798791 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 2.798791 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2350 total number of charged atoms : 2255 net assigned charge : 2.900002 assigned positive charge : 347.7231 centred at (gu) : 91.03059 82.54311 88.14539 assigned negative charge : -344.8238 centred at (gu) : 91.16396 82.99281 88.40785 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 152721 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19999 grid for indexing accessible points = 1.400000 m= 74655 mr = 111627 m= 26409 mr = 60958 m= 6405 mr = 21189 m= 809 mr = 4956 m= 45 mr = 522 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 1072 time to turn everything in is 1.360000 number of dielectric boundary points 61772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 18034 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) : 1.865861 object centre at (A) : 21.54850 7.176000 10.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2233642 -0.1482588 midg,1,midg; midg,igrid,midg 0.1675203 -4.9507327E-02 1,midg,midg; igrid,midg,midg 2.8255686E-02 -0.4765990 gauss-seidel spectral radius is 0.9992284 estimated iterations to convergence 284 setup time was (sec) 1.720000 now iterating at: 15:53:20 rms-change max change #iterations 9.136520 345.7051 at 10iterations 5.297292 125.8355 at 20iterations 3.040735 62.33106 at 30iterations 1.747984 34.11474 at 40iterations 0.9994070 19.62329 at 50iterations 0.5716488 12.41682 at 60iterations 0.3261504 6.372046 at 70iterations 0.1859544 3.903602 at 80iterations 0.1060344 1.973392 at 90iterations 6.0348511E-02 1.176346 at 100iterations 3.4348026E-02 0.6210175 at 110iterations 1.9528043E-02 0.3737774 at 120iterations 1.1127091E-02 0.2367878 at 130iterations 6.3323416E-03 0.1261730 at 140iterations 3.6095453E-03 7.1202278E-02 at 150iterations 2.0666933E-03 4.2726517E-02 at 160iterations 1.1862611E-03 2.3509026E-02 at 170iterations 6.8569731E-04 1.3824463E-02 at 180iterations finished qdiffx linear iterations at : 15:53:34 total time elapsed so far: 15.26000 # loops : 180 mean,max change (kT/e) : 6.8569731E-04 1.3824463E-02 energy calculations done at 15.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.44000 DelPhi exited at 15:53:34 15.444u 0.278s 0:15.99 98.2% 0+0k 0+0io 0pf+0w