Mon Oct 10 14:19:02 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 Mon Oct 10 2011 at 14:19:02 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1159 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: HIT 58 has a net charge of 0.5140 !!! WARNING: SEP 72 has a net charge of -0.4750 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: 0.8436418 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): -0.8750000 41.32300 ymin,ymax (A): -0.1040000 36.91600 zmin,zma (A): 7.131999 45.01200 x,y,z range (A): 42.19800 37.02000 37.88000 scale (grids/A): 0.8436418 object centre (A): 20.22400 18.40600 26.07200 number of atom coordinates read : 1159 total number of charged atoms : 1027 net assigned charge : 1.064005 assigned positive charge : 173.0831 centred at (gu) : 90.87952 90.17826 89.15482 assigned negative charge : -172.0190 centred at (gu) : 90.89194 90.28769 89.25854 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5783 nv = 96 ne = 84 npr = 22813 no. pairs analyzed = 22813 no. exposed pairs = 1487 no. arc points = 10832 no. surface atoms = 503 nbur = 656 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 3169 m= 8 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.2500000 number of dielectric boundary points 2973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 664 ## 71 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6766879E-07 -1.9915183E-07 midg,1,midg; midg,igrid,midg 4.9660633E-07 -2.5981529E-07 1,midg,midg; igrid,midg,midg 1.5348209E-07 1.0327407E-07 gauss-seidel spectral radius is 0.9925663 estimated iterations to convergence 94 setup time was (sec) 0.5000000 now iterating at: 14:19:03 rms-change max change #iterations 0.3040830 52.13992 at 10iterations 5.0909143E-02 7.277588 at 20iterations 8.7927841E-03 1.159676 at 30iterations 1.4797525E-03 0.2238750 at 40iterations 2.5214837E-04 4.6182632E-02 at 50iterations finished qdiffx linear iterations at : 14:19:05 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.5214837E-04 4.6182632E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 14:19:06 3.481u 0.180s 0:04.52 80.9% 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 14:19:06 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1159 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: HIT 58 has a net charge of 0.5140 !!! WARNING: SEP 72 has a net charge of -0.4750 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: 2.530926 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): -0.8750000 41.32300 ymin,ymax (A): -0.1040000 36.91600 zmin,zma (A): 7.131999 45.01200 x,y,z range (A): 42.19800 37.02000 37.88000 scale (grids/A): 2.530926 object centre (A): 20.22400 18.40600 26.07200 number of atom coordinates read : 1159 total number of charged atoms : 1027 net assigned charge : 1.064005 assigned positive charge : 173.0831 centred at (gu) : 92.63847 90.53482 87.46452 assigned negative charge : -172.0190 centred at (gu) : 92.67588 90.86314 87.77565 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10832 grid for indexing accessible points = 1.400000 m= 24507 mr = 39641 m= 6226 mr = 18900 m= 917 mr = 4604 m= 52 mr = 591 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2167 time to turn everything in is 0.4900000 number of dielectric boundary points 27235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 8207 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) : 0.8436418 object centre at (A) : 20.22400 18.40600 26.07200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0060570E-02 -9.8364530E-03 midg,1,midg; midg,igrid,midg 3.0820537E-02 -1.8989975E-02 1,midg,midg; igrid,midg,midg -5.6868826E-06 1.1878702E-02 gauss-seidel spectral radius is 0.9990468 estimated iterations to convergence 256 setup time was (sec) 0.8000000 now iterating at: 14:19:07 rms-change max change #iterations 4.678310 279.2083 at 10iterations 2.474785 118.8951 at 20iterations 1.306888 43.37069 at 30iterations 0.6913967 22.59453 at 40iterations 0.3653989 11.57563 at 50iterations 0.1942581 6.812912 at 60iterations 0.1029359 3.322114 at 70iterations 5.4564007E-02 1.644804 at 80iterations 2.8789641E-02 0.8815117 at 90iterations 1.5320174E-02 0.5313148 at 100iterations 8.1085581E-03 0.2604752 at 110iterations 4.3041361E-03 0.1365936 at 120iterations finished qdiffx linear iterations at : 14:19:14 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 4.3041361E-03 0.1365936 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 14:19:15 7.836u 0.205s 0:08.39 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 Mon Oct 10 2011 at 14:19:15 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1159 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: HIT 58 has a net charge of 0.5140 !!! WARNING: SEP 72 has a net charge of -0.4750 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: 3.796388 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): -0.8750000 41.32300 ymin,ymax (A): -0.1040000 36.91600 zmin,zma (A): 7.131999 45.01200 x,y,z range (A): 42.19800 37.02000 37.88000 scale (grids/A): 3.796388 object centre (A): 20.22400 18.40600 26.07200 number of atom coordinates read : 1159 total number of charged atoms : 1027 net assigned charge : 1.064005 assigned positive charge : 173.0831 centred at (gu) : 93.95773 90.80233 86.19672 assigned negative charge : -172.0190 centred at (gu) : 94.01380 91.29475 86.66354 start vw surface at 0.1100000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 136184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10832 grid for indexing accessible points = 1.400000 m= 72780 mr = 95325 m= 34110 mr = 60648 m= 12487 mr = 28872 m= 3602 mr = 10241 m= 653 mr = 2937 m= 52 mr = 462 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 7723 time to turn everything in is 1.580000 number of dielectric boundary points 61361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 8216 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) : 2.530926 object centre at (A) : 20.22400 18.40600 26.07200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3983023 -5.4865126E-02 midg,1,midg; midg,igrid,midg 0.2189869 -8.7468669E-02 1,midg,midg; igrid,midg,midg -2.5574053E-02 -1.2980538E-02 gauss-seidel spectral radius is 0.9993346 estimated iterations to convergence 306 setup time was (sec) 1.890000 now iterating at: 14:19:17 rms-change max change #iterations 9.578936 247.2886 at 10iterations 5.649349 132.6016 at 20iterations 3.337365 61.77037 at 30iterations 1.968120 37.86649 at 40iterations 1.161317 26.85825 at 50iterations 0.6831430 12.83396 at 60iterations 0.4047424 7.882618 at 70iterations 0.2373929 4.185959 at 80iterations 0.1401751 2.441578 at 90iterations 8.2723282E-02 1.461442 at 100iterations 4.8737988E-02 0.8660126 at 110iterations 2.8737016E-02 0.5272884 at 120iterations 1.6987192E-02 0.2940483 at 130iterations 1.0052147E-02 0.1916275 at 140iterations 5.9378105E-03 0.1083088 at 150iterations 3.5035971E-03 6.8065643E-02 at 160iterations 2.0641305E-03 3.7590027E-02 at 170iterations 1.2188284E-03 2.1492004E-02 at 180iterations finished qdiffx linear iterations at : 14:19:28 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.2188284E-03 2.1492004E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 14:19:29 12.927u 0.242s 0:13.85 95.0% 0+0k 0+0io 0pf+0w