Sat Oct 8 15:46:22 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 15:46:22 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2274 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6464148 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): -17.84900 30.71000 ymin,ymax (A): 4.324000 49.87700 zmin,zma (A): -18.76400 36.30900 x,y,z range (A): 48.55900 45.55300 55.07300 scale (grids/A): 0.6464148 object centre (A): 6.430500 27.10050 8.772499 number of atom coordinates read : 2274 total number of charged atoms : 2209 net assigned charge : 3.806004 assigned positive charge : 340.0512 centred at (gu) : 89.02818 91.08237 90.21581 assigned negative charge : -336.2459 centred at (gu) : 89.01527 90.98699 90.25131 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6517 nv = 96 ne = 84 npr = 45132 no. pairs analyzed = 45132 no. exposed pairs = 2891 no. arc points = 19937 no. surface atoms = 983 nbur = 1291 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3613 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2700000 number of dielectric boundary points 3258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1925 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7764 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0297915E-08 2.3464592E-09 midg,1,midg; midg,igrid,midg -3.9168735E-09 2.2492431E-08 1,midg,midg; igrid,midg,midg 6.0574972E-09 6.6158892E-09 gauss-seidel spectral radius is 0.9875741 estimated iterations to convergence 73 setup time was (sec) 0.4800000 now iterating at: 15:46:23 rms-change max change #iterations 0.1405115 20.46692 at 10iterations 1.4393468E-02 2.152196 at 20iterations 1.4784487E-03 0.2563562 at 30iterations 1.5891458E-04 2.6475906E-02 at 40iterations 2.1132753E-05 2.9449463E-03 at 50iterations finished qdiffx linear iterations at : 15:46:25 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 2.1132753E-05 2.9449463E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 15:46:26 3.073u 0.157s 0:03.57 90.1% 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 15:46:26 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2274 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.939244 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): -17.84900 30.71000 ymin,ymax (A): 4.324000 49.87700 zmin,zma (A): -18.76400 36.30900 x,y,z range (A): 48.55900 45.55300 55.07300 scale (grids/A): 1.939244 object centre (A): 6.430500 27.10050 8.772499 number of atom coordinates read : 2274 total number of charged atoms : 2209 net assigned charge : 3.806004 assigned positive charge : 340.0512 centred at (gu) : 87.08395 93.24665 90.64713 assigned negative charge : -336.2459 centred at (gu) : 87.04578 92.96100 90.75405 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19937 grid for indexing accessible points = 1.400000 m= 26428 mr = 48559 m= 4814 mr = 19661 m= 285 mr = 3217 m= 8 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 419 time to turn everything in is 0.5000000 number of dielectric boundary points 29914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 17421 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) : 0.6464148 object centre at (A) : 6.430500 27.10050 8.772499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3634799E-02 5.6149964E-03 midg,1,midg; midg,igrid,midg -2.4827570E-03 2.1609522E-02 1,midg,midg; igrid,midg,midg -4.5225989E-02 1.4223934E-03 gauss-seidel spectral radius is 0.9986525 estimated iterations to convergence 216 setup time was (sec) 0.7600000 now iterating at: 15:46:27 rms-change max change #iterations 4.106033 170.8475 at 10iterations 1.926217 79.10619 at 20iterations 0.9079781 31.01544 at 30iterations 0.4281140 14.66537 at 40iterations 0.2015442 6.931860 at 50iterations 9.5145464E-02 3.187739 at 60iterations 4.4869803E-02 1.492492 at 70iterations 2.1076147E-02 0.6846876 at 80iterations 9.8938169E-03 0.3391564 at 90iterations 4.6878415E-03 0.1388741 at 100iterations 2.2131370E-03 7.5882077E-02 at 110iterations 1.0412317E-03 3.1301498E-02 at 120iterations finished qdiffx linear iterations at : 15:46:33 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 1.0412317E-03 3.1301498E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 15:46:33 6.859u 0.152s 0:07.28 96.1% 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 15:46:33 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2274 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.908866 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): -17.84900 30.71000 ymin,ymax (A): 4.324000 49.87700 zmin,zma (A): -18.76400 36.30900 x,y,z range (A): 48.55900 45.55300 55.07300 scale (grids/A): 2.908866 object centre (A): 6.430500 27.10050 8.772499 number of atom coordinates read : 2274 total number of charged atoms : 2209 net assigned charge : 3.806004 assigned positive charge : 340.0512 centred at (gu) : 85.62594 94.86971 90.97063 assigned negative charge : -336.2459 centred at (gu) : 85.56863 94.44142 91.13108 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 161651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19937 grid for indexing accessible points = 1.400000 m= 83323 mr = 117682 m= 32627 mr = 68470 m= 9032 mr = 26519 m= 1356 mr = 7026 m= 75 mr = 905 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1469 time to turn everything in is 1.250000 number of dielectric boundary points 67444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17671 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) : 1.939244 object centre at (A) : 6.430500 27.10050 8.772499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2740963 6.3002735E-02 midg,1,midg; midg,igrid,midg -5.8211919E-02 0.1578811 1,midg,midg; igrid,midg,midg -0.6303710 -8.8350782E-03 gauss-seidel spectral radius is 0.9992622 estimated iterations to convergence 291 setup time was (sec) 1.510000 now iterating at: 15:46:35 rms-change max change #iterations 9.590667 366.4122 at 10iterations 5.633757 122.5469 at 20iterations 3.291966 80.76775 at 30iterations 1.918642 39.13665 at 40iterations 1.116830 26.33879 at 50iterations 0.6480097 12.50590 at 60iterations 0.3758036 7.270122 at 70iterations 0.2170375 3.925061 at 80iterations 0.1254852 2.406532 at 90iterations 7.2486222E-02 1.326030 at 100iterations 4.1838601E-02 0.7637558 at 110iterations 2.4029607E-02 0.4266596 at 120iterations 1.3866160E-02 0.3062515 at 130iterations 7.9806345E-03 0.1444550 at 140iterations 4.5972457E-03 8.5300446E-02 at 150iterations 2.6501208E-03 4.7090530E-02 at 160iterations 1.5229388E-03 2.9059887E-02 at 170iterations 8.7717286E-04 1.7693520E-02 at 180iterations finished qdiffx linear iterations at : 15:46:44 total time elapsed so far: 10.85000 # loops : 180 mean,max change (kT/e) : 8.7717286E-04 1.7693520E-02 energy calculations done at 10.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 15:46:45 11.027u 0.192s 0:11.54 97.1% 0+0k 0+0io 0pf+0w