Sat Oct 15 14:27:44 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 15 2011 at 14:27:44 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2582 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 0.6461918 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): -21.08900 31.60200 ymin,ymax (A): -10.85400 38.78500 zmin,zma (A): 6.524000 61.61600 x,y,z range (A): 52.69100 49.63900 55.09200 scale (grids/A): 0.6461918 object centre (A): 5.256499 13.96550 34.07000 number of atom coordinates read : 2582 total number of charged atoms : 2442 net assigned charge : -1.999977 assigned positive charge : 389.9876 centred at (gu) : 90.57140 90.59175 90.73669 assigned negative charge : -391.9886 centred at (gu) : 90.65975 90.45029 90.78706 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7489 nv = 96 ne = 84 npr = 50181 no. pairs analyzed = 50181 no. exposed pairs = 3618 no. arc points = 25787 no. surface atoms = 1219 nbur = 1363 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 3767 m= 0 mr = 54 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2000000 number of dielectric boundary points 4107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2485 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8701 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9852172E-09 -1.2274593E-08 midg,1,midg; midg,igrid,midg -2.0639202E-08 1.8153974E-08 1,midg,midg; igrid,midg,midg 7.7013231E-09 -1.7920843E-08 gauss-seidel spectral radius is 0.9876038 estimated iterations to convergence 73 setup time was (sec) 0.4200000 now iterating at: 14:27:45 rms-change max change #iterations 0.1487013 24.80101 at 10iterations 1.4931739E-02 2.257322 at 20iterations 1.5255343E-03 0.2279723 at 30iterations 1.5146467E-04 2.2208214E-02 at 40iterations 1.5695870E-05 2.0904541E-03 at 50iterations finished qdiffx linear iterations at : 14:27:48 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 1.5695870E-05 2.0904541E-03 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 14:27:48 3.821u 0.243s 0:04.32 93.9% 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 Sat Oct 15 2011 at 14:27:48 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2582 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 1.938576 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): -21.08900 31.60200 ymin,ymax (A): -10.85400 38.78500 zmin,zma (A): 6.524000 61.61600 x,y,z range (A): 52.69100 49.63900 55.09200 scale (grids/A): 1.938576 object centre (A): 5.256499 13.96550 34.07000 number of atom coordinates read : 2582 total number of charged atoms : 2442 net assigned charge : -1.999977 assigned positive charge : 389.9876 centred at (gu) : 91.71328 91.77481 92.20972 assigned negative charge : -391.9886 centred at (gu) : 91.97896 91.35069 92.36095 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25787 grid for indexing accessible points = 1.400000 m= 27812 mr = 51821 m= 4613 mr = 19529 m= 370 mr = 2799 m= 11 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 661 time to turn everything in is 0.4000000 number of dielectric boundary points 37828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 19255 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) : 0.6461918 object centre at (A) : 5.256499 13.96550 34.07000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1703556E-02 1.1138766E-02 midg,1,midg; midg,igrid,midg -2.9082732E-02 1.9585755E-02 1,midg,midg; igrid,midg,midg -1.2629418E-02 -5.3459089E-02 gauss-seidel spectral radius is 0.9987010 estimated iterations to convergence 220 setup time was (sec) 0.6600000 now iterating at: 14:27:49 rms-change max change #iterations 4.383757 181.6391 at 10iterations 2.086646 82.98625 at 20iterations 0.9953892 32.83911 at 30iterations 0.4709756 16.52557 at 40iterations 0.2239459 7.508823 at 50iterations 0.1071226 3.605850 at 60iterations 5.0921690E-02 1.620075 at 70iterations 2.4114618E-02 0.7765329 at 80iterations 1.1499871E-02 0.3404579 at 90iterations 5.4831426E-03 0.1698294 at 100iterations 2.6124013E-03 8.5256577E-02 at 110iterations 1.2464250E-03 3.9476395E-02 at 120iterations finished qdiffx linear iterations at : 14:27:57 total time elapsed so far: 8.340000 # loops : 120 mean,max change (kT/e) : 1.2464250E-03 3.9476395E-02 energy calculations done at 8.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 14:27:57 8.474u 0.230s 0:08.99 96.7% 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 Sat Oct 15 2011 at 14:27:57 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2582 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 2.907863 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): -21.08900 31.60200 ymin,ymax (A): -10.85400 38.78500 zmin,zma (A): 6.524000 61.61600 x,y,z range (A): 52.69100 49.63900 55.09200 scale (grids/A): 2.907863 object centre (A): 5.256499 13.96550 34.07000 number of atom coordinates read : 2582 total number of charged atoms : 2442 net assigned charge : -1.999977 assigned positive charge : 389.9876 centred at (gu) : 92.56978 92.66207 93.31439 assigned negative charge : -391.9886 centred at (gu) : 92.96835 92.02599 93.54134 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183177 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25787 grid for indexing accessible points = 1.400000 m= 89517 mr = 126607 m= 32609 mr = 70821 m= 8248 mr = 25367 m= 1522 mr = 5993 m= 140 mr = 1065 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2266 time to turn everything in is 1.040000 number of dielectric boundary points 85321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 19532 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) : 1.938576 object centre at (A) : 5.256499 13.96550 34.07000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3592115 0.4581587 midg,1,midg; midg,igrid,midg -0.2525744 0.2078207 1,midg,midg; igrid,midg,midg -8.3273508E-02 -0.5871788 gauss-seidel spectral radius is 0.9992985 estimated iterations to convergence 298 setup time was (sec) 1.290000 now iterating at: 14:27:59 rms-change max change #iterations 10.47582 400.7770 at 10iterations 6.260152 165.4644 at 20iterations 3.704559 91.85805 at 30iterations 2.183118 46.75357 at 40iterations 1.282010 24.37548 at 50iterations 0.7525159 16.06852 at 60iterations 0.4396855 8.640968 at 70iterations 0.2569731 4.572208 at 80iterations 0.1501059 2.750179 at 90iterations 8.7481357E-02 1.553989 at 100iterations 5.1139761E-02 0.9376030 at 110iterations 2.9726300E-02 0.5262184 at 120iterations 1.7335109E-02 0.3107805 at 130iterations 1.0107401E-02 0.1688387 at 140iterations 5.8844015E-03 0.1000061 at 150iterations 3.4303870E-03 6.3320577E-02 at 160iterations 1.9983600E-03 3.5552979E-02 at 170iterations 1.1662727E-03 2.0889282E-02 at 180iterations finished qdiffx linear iterations at : 14:28:22 total time elapsed so far: 13.66000 # loops : 180 mean,max change (kT/e) : 1.1662727E-03 2.0889282E-02 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 14:28:23 13.799u 0.268s 0:25.26 55.6% 0+0k 0+0io 0pf+0w