Mon Oct 10 17:03:47 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 17:03:47 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2843 !!! WARNING: HIT 107 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6338467 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): -24.77800 31.38700 ymin,ymax (A): 3.741000 50.81100 zmin,zma (A): 0.3750001 55.15800 x,y,z range (A): 56.16500 47.07000 54.78300 scale (grids/A): 0.6338467 object centre (A): 3.304501 27.27600 27.76650 number of atom coordinates read : 2843 total number of charged atoms : 2702 net assigned charge : -2.985967 assigned positive charge : 430.5061 centred at (gu) : 90.54614 90.42720 88.73118 assigned negative charge : -433.4932 centred at (gu) : 90.64596 90.58781 88.63484 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7816 nv = 96 ne = 84 npr = 56146 no. pairs analyzed = 56146 no. exposed pairs = 3823 no. arc points = 26441 no. surface atoms = 1290 nbur = 1553 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 4137 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3900000 number of dielectric boundary points 4047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2616 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9308 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8463965E-08 5.3861764E-09 midg,1,midg; midg,igrid,midg 1.2744851E-08 -2.3322729E-08 1,midg,midg; igrid,midg,midg 6.6619261E-09 -1.6193271E-08 gauss-seidel spectral radius is 0.9871353 estimated iterations to convergence 72 setup time was (sec) 0.6400000 now iterating at: 17:03:48 rms-change max change #iterations 0.1485264 20.57287 at 10iterations 1.4199270E-02 1.874949 at 20iterations 1.3803702E-03 0.1915016 at 30iterations 1.3597781E-04 1.6880035E-02 at 40iterations 1.4190913E-05 2.6245117E-03 at 50iterations finished qdiffx linear iterations at : 17:03:51 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.4190913E-05 2.6245117E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 17:03:52 3.664u 0.226s 0:05.13 75.6% 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 17:03:52 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2843 !!! WARNING: HIT 107 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.901540 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): -24.77800 31.38700 ymin,ymax (A): 3.741000 50.81100 zmin,zma (A): 0.3750001 55.15800 x,y,z range (A): 56.16500 47.07000 54.78300 scale (grids/A): 1.901540 object centre (A): 3.304501 27.27600 27.76650 number of atom coordinates read : 2843 total number of charged atoms : 2702 net assigned charge : -2.985967 assigned positive charge : 430.5061 centred at (gu) : 91.63758 91.28087 86.19262 assigned negative charge : -433.4932 centred at (gu) : 91.93759 91.76299 85.90417 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 83680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26441 grid for indexing accessible points = 1.400000 m= 29185 mr = 56627 m= 4197 mr = 20855 m= 237 mr = 2425 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 315 time to turn everything in is 0.6600000 number of dielectric boundary points 37315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 210 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21299 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) : 0.6338467 object centre at (A) : 3.304501 27.27600 27.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5950485E-04 8.4240017E-03 midg,1,midg; midg,igrid,midg 9.2167463E-03 -3.2416984E-02 1,midg,midg; igrid,midg,midg 2.7672160E-02 -6.6804871E-02 gauss-seidel spectral radius is 0.9986627 estimated iterations to convergence 217 setup time was (sec) 0.9900000 now iterating at: 17:03:53 rms-change max change #iterations 4.511915 175.8202 at 10iterations 2.121763 77.18034 at 20iterations 0.9980084 27.96666 at 30iterations 0.4714036 15.03349 at 40iterations 0.2217884 6.817806 at 50iterations 0.1046608 3.365079 at 60iterations 4.9323849E-02 1.496033 at 70iterations 2.3201790E-02 0.6848869 at 80iterations 1.0947809E-02 0.2976608 at 90iterations 5.1362589E-03 0.1625595 at 100iterations 2.4330919E-03 8.4743500E-02 at 110iterations 1.1475799E-03 3.1982422E-02 at 120iterations finished qdiffx linear iterations at : 17:04:01 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 1.1475799E-03 3.1982422E-02 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.500000 DelPhi exited at 17:04:02 8.501u 0.257s 0:09.95 87.9% 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 17:04:04 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2843 !!! WARNING: HIT 107 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.852310 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): -24.77800 31.38700 ymin,ymax (A): 3.741000 50.81100 zmin,zma (A): 0.3750001 55.15800 x,y,z range (A): 56.16500 47.07000 54.78300 scale (grids/A): 2.852310 object centre (A): 3.304501 27.27600 27.76650 number of atom coordinates read : 2843 total number of charged atoms : 2702 net assigned charge : -2.985967 assigned positive charge : 430.5061 centred at (gu) : 92.45614 91.92112 84.28878 assigned negative charge : -433.4932 centred at (gu) : 92.90647 92.64434 83.85624 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 193583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26441 grid for indexing accessible points = 1.400000 m= 95181 mr = 137684 m= 33195 mr = 76406 m= 7474 mr = 26084 m= 935 mr = 5272 m= 56 mr = 582 m= 0 mr = 16 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 1192 time to turn everything in is 1.640000 number of dielectric boundary points 84380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 21616 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) : 1.901540 object centre at (A) : 3.304501 27.27600 27.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2545638 -0.1837925 midg,1,midg; midg,igrid,midg 5.7273276E-02 -0.2766027 1,midg,midg; igrid,midg,midg 0.4491349 -0.7517297 gauss-seidel spectral radius is 0.9992866 estimated iterations to convergence 295 setup time was (sec) 1.980000 now iterating at: 17:04:07 rms-change max change #iterations 10.69104 410.1581 at 10iterations 6.365868 134.3658 at 20iterations 3.752096 79.37057 at 30iterations 2.209513 47.86584 at 40iterations 1.294579 24.57700 at 50iterations 0.7564795 13.53598 at 60iterations 0.4419824 8.336941 at 70iterations 0.2574924 4.571898 at 80iterations 0.1502327 2.637938 at 90iterations 8.7131172E-02 1.673100 at 100iterations 5.0823681E-02 0.8310623 at 110iterations 2.9556131E-02 0.5270631 at 120iterations 1.7175054E-02 0.2942905 at 130iterations 9.9601485E-03 0.1655273 at 140iterations 5.7867877E-03 0.1078424 at 150iterations 3.3605546E-03 5.6678772E-02 at 160iterations 1.9533450E-03 3.3693314E-02 at 170iterations 1.1345969E-03 2.0389557E-02 at 180iterations finished qdiffx linear iterations at : 17:04:18 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 1.1345969E-03 2.0389557E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 17:04:19 13.180u 0.245s 0:14.86 90.3% 0+0k 0+0io 0pf+0w