Tue Nov 22 14:12:16 PST 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 Tue Nov 22 2011 at 14:12:19 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 0.6251097 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): -35.21400 9.832000 ymin,ymax (A): 1.186000 42.74900 zmin,zma (A): -0.2710000 56.67900 x,y,z range (A): 45.04600 41.56300 56.95000 scale (grids/A): 0.6251097 object centre (A): -12.69100 21.96750 28.20400 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 292.2219 centred at (gu) : 90.50344 89.05344 89.79641 assigned negative charge : -289.2222 centred at (gu) : 90.43085 89.20071 89.81019 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5244 nv = 96 ne = 84 npr = 39831 no. pairs analyzed = 39831 no. exposed pairs = 2496 no. arc points = 17157 no. surface atoms = 850 nbur = 1110 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 2893 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6165 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6554892E-09 1.8402649E-09 midg,1,midg; midg,igrid,midg 1.3587873E-08 -4.7389159E-09 1,midg,midg; igrid,midg,midg -1.3153525E-09 7.6382261E-09 gauss-seidel spectral radius is 0.9866912 estimated iterations to convergence 71 setup time was (sec) 0.4600000 now iterating at: 14:12:21 rms-change max change #iterations 0.1136757 19.29421 at 10iterations 1.0711575E-02 1.747782 at 20iterations 9.8031247E-04 0.1766529 at 30iterations 9.2840361E-05 1.6064644E-02 at 40iterations 8.5549354E-06 1.4190674E-03 at 50iterations finished qdiffx linear iterations at : 14:12:28 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 8.5549354E-06 1.4190674E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 14:12:29 3.284u 0.223s 0:10.01 34.9% 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 Tue Nov 22 2011 at 14:12:30 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 1.875329 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): -35.21400 9.832000 ymin,ymax (A): 1.186000 42.74900 zmin,zma (A): -0.2710000 56.67900 x,y,z range (A): 45.04600 41.56300 56.95000 scale (grids/A): 1.875329 object centre (A): -12.69100 21.96750 28.20400 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 292.2219 centred at (gu) : 91.51031 87.16031 89.38946 assigned negative charge : -289.2222 centred at (gu) : 91.29260 87.60243 89.43076 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 56231 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17157 grid for indexing accessible points = 1.400000 m= 20817 mr = 38667 m= 3332 mr = 15703 m= 199 mr = 2218 m= 1 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 23898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14377 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) : 0.6251097 object centre at (A) : -12.69100 21.96750 28.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8712206E-02 2.5188413E-02 midg,1,midg; midg,igrid,midg 6.8412889E-03 -6.6018505E-03 1,midg,midg; igrid,midg,midg -4.1759717E-03 -2.1449868E-03 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 0.7000000 now iterating at: 14:12:33 rms-change max change #iterations 3.507096 165.7482 at 10iterations 1.585897 63.12088 at 20iterations 0.7215306 25.84669 at 30iterations 0.3264001 13.01600 at 40iterations 0.1481077 5.218118 at 50iterations 6.7008257E-02 2.472052 at 60iterations 3.0453039E-02 1.133408 at 70iterations 1.3775256E-02 0.4761572 at 80iterations 6.2617478E-03 0.2396102 at 90iterations 2.8430077E-03 0.1063643 at 100iterations 1.2877076E-03 4.5260668E-02 at 110iterations 5.8757735E-04 2.3651838E-02 at 120iterations finished qdiffx linear iterations at : 14:12:45 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 5.8757735E-04 2.3651838E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 14:12:48 7.213u 0.190s 0:17.91 41.3% 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 Tue Nov 22 2011 at 14:12:51 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 2.812994 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): -35.21400 9.832000 ymin,ymax (A): 1.186000 42.74900 zmin,zma (A): -0.2710000 56.67900 x,y,z range (A): 45.04600 41.56300 56.95000 scale (grids/A): 2.812994 object centre (A): -12.69100 21.96750 28.20400 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 292.2219 centred at (gu) : 92.26543 85.74051 89.08427 assigned negative charge : -289.2222 centred at (gu) : 91.93908 86.40359 89.14618 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 129629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17157 grid for indexing accessible points = 1.400000 m= 66551 mr = 93075 m= 24906 mr = 55124 m= 6167 mr = 20642 m= 859 mr = 4841 m= 48 mr = 650 m= 0 mr = 24 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 53804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 14623 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) : 1.875329 object centre at (A) : -12.69100 21.96750 28.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8112245E-02 0.1717005 midg,1,midg; midg,igrid,midg -8.8006845E-03 -8.2964189E-02 1,midg,midg; igrid,midg,midg -8.2450554E-02 -5.8907364E-02 gauss-seidel spectral radius is 0.9992098 estimated iterations to convergence 281 setup time was (sec) 1.250000 now iterating at: 14:12:58 rms-change max change #iterations 8.311297 327.3342 at 10iterations 4.741063 133.3120 at 20iterations 2.681006 78.23732 at 30iterations 1.516208 33.58130 at 40iterations 0.8552477 19.80535 at 50iterations 0.4822361 10.04198 at 60iterations 0.2703518 6.431679 at 70iterations 0.1528099 3.257243 at 80iterations 8.6019866E-02 1.869507 at 90iterations 4.8288532E-02 1.062363 at 100iterations 2.7214551E-02 0.6004152 at 110iterations 1.5310137E-02 0.3132007 at 120iterations 8.6110309E-03 0.1719208 at 130iterations 4.8484630E-03 0.1204576 at 140iterations 2.7263379E-03 5.7106018E-02 at 150iterations 1.5383434E-03 3.5060883E-02 at 160iterations 8.6545048E-04 1.7422676E-02 at 170iterations 4.8764664E-04 1.0211945E-02 at 180iterations finished qdiffx linear iterations at : 14:13:26 total time elapsed so far: 10.50000 # loops : 180 mean,max change (kT/e) : 4.8764664E-04 1.0211945E-02 energy calculations done at 10.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 14:13:32 10.670u 0.169s 0:40.66 26.6% 0+0k 0+0io 0pf+0w