Tue Oct 11 08:22:31 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 Tue Oct 11 2011 at 08:22:31 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 !!! WARNING: HIT 113 has a net charge of 0.5140 !!! WARNING: HIT 115 has a net charge of 0.5140 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: 0.5699556 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): 59.66100 111.2680 ymin,ymax (A): 26.61800 89.07900 zmin,zma (A): 25.40500 86.38100 x,y,z range (A): 51.60700 62.46100 60.97600 scale (grids/A): 0.5699556 object centre (A): 85.46450 57.84850 55.89300 number of atom coordinates read : 3382 total number of charged atoms : 3232 net assigned charge : 6.528036 assigned positive charge : 525.1302 centred at (gu) : 87.80424 91.12232 91.39857 assigned negative charge : -518.6039 centred at (gu) : 87.84878 91.09506 91.54550 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7708 nv = 96 ne = 84 npr = 62974 no. pairs analyzed = 62974 no. exposed pairs = 4867 no. arc points = 34515 no. surface atoms = 1630 nbur = 1752 mkacc time = 0.1000000 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 = 1.484000 m= 375 mr = 3742 m= 0 mr = 35 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3571 ## 422 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6019427E-09 -2.4192266E-09 midg,1,midg; midg,igrid,midg 4.0125919E-10 1.9553072E-09 1,midg,midg; igrid,midg,midg 3.0594156E-09 1.3152901E-10 gauss-seidel spectral radius is 0.9841686 estimated iterations to convergence 65 setup time was (sec) 0.4200000 now iterating at: 08:22:31 rms-change max change #iterations 0.1009226 15.47141 at 10iterations 7.5560808E-03 1.167991 at 20iterations 6.4889312E-04 0.1004620 at 30iterations 1.1032733E-04 1.5446663E-02 at 40iterations 3.2727730E-05 4.2285919E-03 at 50iterations finished qdiffx linear iterations at : 08:22:35 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 3.2727730E-05 4.2285919E-03 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 08:22:35 3.767u 0.178s 0:04.25 92.4% 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 Tue Oct 11 2011 at 08:22:35 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 !!! WARNING: HIT 113 has a net charge of 0.5140 !!! WARNING: HIT 115 has a net charge of 0.5140 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: 1.709867 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): 59.66100 111.2680 ymin,ymax (A): 26.61800 89.07900 zmin,zma (A): 25.40500 86.38100 x,y,z range (A): 51.60700 62.46100 60.97600 scale (grids/A): 1.709867 object centre (A): 85.46450 57.84850 55.89300 number of atom coordinates read : 3382 total number of charged atoms : 3232 net assigned charge : 6.528036 assigned positive charge : 525.1302 centred at (gu) : 83.41187 93.36570 94.19472 assigned negative charge : -518.6039 centred at (gu) : 83.54617 93.28471 94.63607 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34515 grid for indexing accessible points = 1.400000 m= 28435 mr = 55474 m= 3706 mr = 19068 m= 151 mr = 1850 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 40060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 25021 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) : 0.5699556 object centre at (A) : 85.46450 57.84850 55.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2755525E-03 -2.7002968E-02 midg,1,midg; midg,igrid,midg 2.3151971E-02 3.9458741E-02 1,midg,midg; igrid,midg,midg 2.0868493E-02 8.9884939E-04 gauss-seidel spectral radius is 0.9984129 estimated iterations to convergence 199 setup time was (sec) 0.6200000 now iterating at: 08:22:36 rms-change max change #iterations 4.058566 172.6617 at 10iterations 1.775911 67.07567 at 20iterations 0.7809325 26.27025 at 30iterations 0.3429939 11.37404 at 40iterations 0.1514028 5.038929 at 50iterations 6.6385001E-02 2.201554 at 60iterations 2.9412189E-02 0.9761086 at 70iterations 1.2951232E-02 0.4399986 at 80iterations 5.6977947E-03 0.2104511 at 90iterations 2.5353197E-03 8.8245511E-02 at 100iterations 1.1225208E-03 3.9903164E-02 at 110iterations 5.0262985E-04 1.5930176E-02 at 120iterations finished qdiffx linear iterations at : 08:22:43 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 5.0262985E-04 1.5930176E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 08:22:44 7.921u 0.204s 0:08.77 92.5% 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 Tue Oct 11 2011 at 08:22:44 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3382 !!! WARNING: HIT 113 has a net charge of 0.5140 !!! WARNING: HIT 115 has a net charge of 0.5140 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: 2.564800 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): 59.66100 111.2680 ymin,ymax (A): 26.61800 89.07900 zmin,zma (A): 25.40500 86.38100 x,y,z range (A): 51.60700 62.46100 60.97600 scale (grids/A): 2.564800 object centre (A): 85.46450 57.84850 55.89300 number of atom coordinates read : 3382 total number of charged atoms : 3232 net assigned charge : 6.528036 assigned positive charge : 525.1302 centred at (gu) : 80.11771 95.04826 96.29181 assigned negative charge : -518.6039 centred at (gu) : 80.31913 94.92690 96.95413 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 194863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34515 grid for indexing accessible points = 1.400000 m= 94308 mr = 135953 m= 30453 mr = 73134 m= 6033 mr = 22542 m= 578 mr = 3916 m= 26 mr = 260 m= 0 mr = 6 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 90450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 25847 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) : 1.709867 object centre at (A) : 85.46450 57.84850 55.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3263079E-02 -0.1907179 midg,1,midg; midg,igrid,midg 0.3071674 0.5565039 1,midg,midg; igrid,midg,midg 0.3248532 2.6583697E-03 gauss-seidel spectral radius is 0.9992238 estimated iterations to convergence 283 setup time was (sec) 1.260000 now iterating at: 08:22:45 rms-change max change #iterations 10.20510 326.0306 at 10iterations 5.986090 144.6371 at 20iterations 3.473643 67.47383 at 30iterations 2.008402 47.74049 at 40iterations 1.155386 25.11235 at 50iterations 0.6625063 12.65241 at 60iterations 0.3783977 7.835157 at 70iterations 0.2162354 4.373264 at 80iterations 0.1233644 2.886400 at 90iterations 7.0247181E-02 1.418052 at 100iterations 3.9992485E-02 0.8595428 at 110iterations 2.2710223E-02 0.4493256 at 120iterations 1.2909121E-02 0.2440939 at 130iterations 7.3328563E-03 0.1532516 at 140iterations 4.1663996E-03 7.5843811E-02 at 150iterations 2.3596610E-03 4.0956497E-02 at 160iterations 1.3393479E-03 2.4511337E-02 at 170iterations 7.6142425E-04 1.4754295E-02 at 180iterations finished qdiffx linear iterations at : 08:22:57 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 7.6142425E-04 1.4754295E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 08:22:58 13.282u 0.217s 0:13.92 96.9% 0+0k 0+0io 0pf+0w