Mon Oct 10 17:02:55 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+sph.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 Mon Oct 10 2011 at 17:02:55 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 = 2741 !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6279435 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): 14.42800 71.12100 ymin,ymax (A): 3.787000 50.60200 zmin,zma (A): 6.807000 61.46400 x,y,z range (A): 56.69300 46.81500 54.65700 scale (grids/A): 0.6279435 object centre (A): 42.77450 27.19450 34.13550 number of atom coordinates read : 2741 total number of charged atoms : 2602 net assigned charge : -3.587964 assigned positive charge : 407.3345 centred at (gu) : 89.02805 90.78277 91.54988 assigned negative charge : -410.9234 centred at (gu) : 88.93558 90.93229 91.63735 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7344 nv = 96 ne = 84 npr = 54805 no. pairs analyzed = 54805 no. exposed pairs = 3542 no. arc points = 25187 no. surface atoms = 1194 nbur = 1547 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3872 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2506 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0244611E-09 -1.5569594E-08 midg,1,midg; midg,igrid,midg 8.0758280E-09 -1.9809395E-08 1,midg,midg; igrid,midg,midg -1.4254740E-08 3.7988901E-09 gauss-seidel spectral radius is 0.9868841 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 17:02:56 rms-change max change #iterations 0.1327700 19.82634 at 10iterations 1.2852822E-02 1.652012 at 20iterations 1.2121028E-03 0.1667957 at 30iterations 1.1609736E-04 1.7601967E-02 at 40iterations 1.1525210E-05 1.5683174E-03 at 50iterations finished qdiffx linear iterations at : 17:02:59 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.1525210E-05 1.5683174E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 17:02:59 3.408u 0.174s 0:04.25 84.0% 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 Mon Oct 10 2011 at 17:02:59 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 = 2741 !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 has a net charge of -0.2720 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: 1.883830 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): 14.42800 71.12100 ymin,ymax (A): 3.787000 50.60200 zmin,zma (A): 6.807000 61.46400 x,y,z range (A): 56.69300 46.81500 54.65700 scale (grids/A): 1.883830 object centre (A): 42.77450 27.19450 34.13550 number of atom coordinates read : 2741 total number of charged atoms : 2602 net assigned charge : -3.587964 assigned positive charge : 407.3345 centred at (gu) : 87.08346 92.34755 94.64883 assigned negative charge : -410.9234 centred at (gu) : 86.80638 92.79659 94.91196 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25187 grid for indexing accessible points = 1.400000 m= 27265 mr = 54139 m= 3902 mr = 19569 m= 185 mr = 2326 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 790 time to turn everything in is 0.3900000 number of dielectric boundary points 34821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20422 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) : 0.6279435 object centre at (A) : 42.77450 27.19450 34.13550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1445863E-02 7.9394685E-04 midg,1,midg; midg,igrid,midg 1.1577253E-02 -3.3189379E-02 1,midg,midg; igrid,midg,midg -4.9097024E-02 2.5754441E-02 gauss-seidel spectral radius is 0.9986226 estimated iterations to convergence 214 setup time was (sec) 0.6100000 now iterating at: 17:03:00 rms-change max change #iterations 4.281749 184.4093 at 10iterations 1.990620 75.28523 at 20iterations 0.9281837 37.98411 at 30iterations 0.4339734 13.49953 at 40iterations 0.2018434 6.435731 at 50iterations 9.4148457E-02 2.811387 at 60iterations 4.3981019E-02 1.308216 at 70iterations 2.0517372E-02 0.7066040 at 80iterations 9.5637012E-03 0.3292065 at 90iterations 4.4563566E-03 0.1318417 at 100iterations 2.0761001E-03 6.1765671E-02 at 110iterations 9.7004685E-04 3.5699844E-02 at 120iterations finished qdiffx linear iterations at : 17:03:08 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 9.7004685E-04 3.5699844E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 17:03:09 8.794u 0.197s 0:09.37 95.8% 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 Mon Oct 10 2011 at 17:03:09 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 = 2741 !!! WARNING: ASN 14 has a net charge of -0.2720 !!! WARNING: GLY 31 has a net charge of -0.2720 !!! WARNING: GLY 170 has a net charge of -0.2720 !!! WARNING: LEU 353 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.825746 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): 14.42800 71.12100 ymin,ymax (A): 3.787000 50.60200 zmin,zma (A): 6.807000 61.46400 x,y,z range (A): 56.69300 46.81500 54.65700 scale (grids/A): 2.825746 object centre (A): 42.77450 27.19450 34.13550 number of atom coordinates read : 2741 total number of charged atoms : 2602 net assigned charge : -3.587964 assigned positive charge : 407.3345 centred at (gu) : 85.62504 93.52105 96.97305 assigned negative charge : -410.9234 centred at (gu) : 85.20955 94.19489 97.36788 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 184406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25187 grid for indexing accessible points = 1.400000 m= 89635 mr = 131724 m= 30680 mr = 72437 m= 6732 mr = 24146 m= 818 mr = 4941 m= 44 mr = 542 m= 0 mr = 10 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2935 time to turn everything in is 1.040000 number of dielectric boundary points 78515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 20816 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) : 1.883830 object centre at (A) : 42.77450 27.19450 34.13550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4234286 0.2262906 midg,1,midg; midg,igrid,midg 0.1515409 -0.3156573 1,midg,midg; igrid,midg,midg -0.6519553 0.3450488 gauss-seidel spectral radius is 0.9992747 estimated iterations to convergence 293 setup time was (sec) 1.320000 now iterating at: 17:03:10 rms-change max change #iterations 10.30912 409.9766 at 10iterations 6.122971 147.5139 at 20iterations 3.582569 81.72898 at 30iterations 2.104170 43.60984 at 40iterations 1.225117 25.48578 at 50iterations 0.7117244 14.35228 at 60iterations 0.4132083 8.900375 at 70iterations 0.2400004 4.546736 at 80iterations 0.1392267 2.709373 at 90iterations 8.0724828E-02 1.481190 at 100iterations 4.6521515E-02 0.7926664 at 110iterations 2.6903724E-02 0.4889889 at 120iterations 1.5563296E-02 0.2921934 at 130iterations 8.9855846E-03 0.1570778 at 140iterations 5.1938435E-03 9.8552704E-02 at 150iterations 3.0015986E-03 6.5040588E-02 at 160iterations 1.7338183E-03 3.0388832E-02 at 170iterations 1.0036449E-03 1.9136429E-02 at 180iterations finished qdiffx linear iterations at : 17:03:22 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 1.0036449E-03 1.9136429E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 17:03:23 13.150u 0.277s 0:14.08 95.3% 0+0k 0+0io 0pf+0w