Mon Oct 10 10:29:35 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 10:29:35 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: 412 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3571 !!! WARNING: GLM 151 has a net charge of -0.0940 !!! WARNING: MG1 1012 has a net charge of 1.4000 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: 0.5873522 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): 36.04800 86.24900 ymin,ymax (A): 25.68100 85.93200 zmin,zma (A): -93.14200 -32.53100 x,y,z range (A): 50.20100 60.25100 60.61100 scale (grids/A): 0.5873522 object centre (A): 61.14850 55.80650 -62.83650 number of atom coordinates read : 3571 total number of charged atoms : 2986 net assigned charge : 17.80602 assigned positive charge : 465.1783 centred at (gu) : 91.75045 89.33961 89.00220 assigned negative charge : -447.3735 centred at (gu) : 91.81809 89.29671 88.89127 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8265 nv = 96 ne = 84 npr = 72298 no. pairs analyzed = 72298 no. exposed pairs = 5221 no. arc points = 36502 no. surface atoms = 1731 nbur = 1840 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 457 mr = 3947 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.4000000 number of dielectric boundary points 4739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3075 ## 333 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3549032E-09 6.4874675E-09 midg,1,midg; midg,igrid,midg 4.4673771E-09 5.3980056E-09 1,midg,midg; igrid,midg,midg 4.6876312E-09 4.6337512E-09 gauss-seidel spectral radius is 0.9851040 estimated iterations to convergence 67 setup time was (sec) 0.6700000 now iterating at: 10:29:36 rms-change max change #iterations 0.1102042 15.62671 at 10iterations 9.1095464E-03 1.657682 at 20iterations 8.4773579E-04 0.1230888 at 30iterations 1.5350722E-04 2.5315285E-02 at 40iterations 4.2542619E-05 7.8248978E-03 at 50iterations finished qdiffx linear iterations at : 10:29:39 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 4.2542619E-05 7.8248978E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 10:29:40 3.746u 0.200s 0:04.21 93.5% 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 10:29:40 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: 412 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3571 !!! WARNING: GLM 151 has a net charge of -0.0940 !!! WARNING: MG1 1012 has a net charge of 1.4000 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: 1.762056 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): 36.04800 86.24900 ymin,ymax (A): 25.68100 85.93200 zmin,zma (A): -93.14200 -32.53100 x,y,z range (A): 50.20100 60.25100 60.61100 scale (grids/A): 1.762056 object centre (A): 61.14850 55.80650 -62.83650 number of atom coordinates read : 3571 total number of charged atoms : 2986 net assigned charge : 17.80602 assigned positive charge : 465.1783 centred at (gu) : 95.25048 88.01782 87.00573 assigned negative charge : -447.3735 centred at (gu) : 95.45419 87.89007 86.67354 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 88875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36502 grid for indexing accessible points = 1.400000 m= 29620 mr = 56574 m= 4393 mr = 20113 m= 167 mr = 2402 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 405 time to turn everything in is 0.6800000 number of dielectric boundary points 43937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 245 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 23220 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) : 0.5873522 object centre at (A) : 61.14850 55.80650 -62.83650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2619050E-02 2.3568476E-02 midg,1,midg; midg,igrid,midg 4.1472275E-02 4.2306285E-02 1,midg,midg; igrid,midg,midg 2.0118384E-02 1.0804383E-02 gauss-seidel spectral radius is 0.9985404 estimated iterations to convergence 208 setup time was (sec) 0.9900000 now iterating at: 10:29:41 rms-change max change #iterations 4.048040 172.5495 at 10iterations 1.840199 71.73427 at 20iterations 0.8375389 29.01608 at 30iterations 0.3810749 12.33198 at 40iterations 0.1741393 5.681745 at 50iterations 7.9338416E-02 2.371094 at 60iterations 3.6113389E-02 1.091073 at 70iterations 1.6520405E-02 0.5543938 at 80iterations 7.5388523E-03 0.2235374 at 90iterations 3.4398213E-03 0.1172752 at 100iterations 1.5702647E-03 4.6670914E-02 at 110iterations 7.1765244E-04 2.0172119E-02 at 120iterations finished qdiffx linear iterations at : 10:29:48 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 7.1765244E-04 2.0172119E-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) 8.480000 DelPhi exited at 10:29:49 8.483u 0.255s 0:09.00 97.0% 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 10:29:49 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: 412 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3571 !!! WARNING: GLM 151 has a net charge of -0.0940 !!! WARNING: MG1 1012 has a net charge of 1.4000 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: 2.643085 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): 36.04800 86.24900 ymin,ymax (A): 25.68100 85.93200 zmin,zma (A): -93.14200 -32.53100 x,y,z range (A): 50.20100 60.25100 60.61100 scale (grids/A): 2.643085 object centre (A): 61.14850 55.80650 -62.83650 number of atom coordinates read : 3571 total number of charged atoms : 2986 net assigned charge : 17.80602 assigned positive charge : 465.1783 centred at (gu) : 97.87560 87.02663 85.50855 assigned negative charge : -447.3735 centred at (gu) : 98.18125 86.83509 85.01007 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 205635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36502 grid for indexing accessible points = 1.400000 m= 96317 mr = 139079 m= 32919 mr = 74281 m= 7495 mr = 24948 m= 825 mr = 5290 m= 21 mr = 458 m= 0 mr = 3 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 1436 time to turn everything in is 1.680000 number of dielectric boundary points 99153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 23880 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) : 1.762056 object centre at (A) : 61.14850 55.80650 -62.83650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9921731E-02 0.3065078 midg,1,midg; midg,igrid,midg 0.6432235 0.4002199 1,midg,midg; igrid,midg,midg 0.2432770 5.0581198E-02 gauss-seidel spectral radius is 0.9992775 estimated iterations to convergence 294 setup time was (sec) 2.030000 now iterating at: 10:29:51 rms-change max change #iterations 10.03245 272.6113 at 10iterations 6.001976 162.1870 at 20iterations 3.535810 79.95213 at 30iterations 2.081124 40.06966 at 40iterations 1.218334 26.25097 at 50iterations 0.7136399 14.29762 at 60iterations 0.4144271 7.932959 at 70iterations 0.2413943 4.966506 at 80iterations 0.1402128 2.721052 at 90iterations 8.1473559E-02 1.502327 at 100iterations 4.7258139E-02 0.8843827 at 110iterations 2.7417144E-02 0.5755253 at 120iterations 1.5869819E-02 0.2780838 at 130iterations 9.1819186E-03 0.1615343 at 140iterations 5.3221923E-03 0.1028824 at 150iterations 3.0859895E-03 5.5927277E-02 at 160iterations 1.7788174E-03 3.2270432E-02 at 170iterations 1.0310091E-03 1.9275665E-02 at 180iterations finished qdiffx linear iterations at : 10:30:03 total time elapsed so far: 14.12000 # loops : 180 mean,max change (kT/e) : 1.0310091E-03 1.9275665E-02 energy calculations done at 14.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.31000 DelPhi exited at 10:30:04 14.316u 0.264s 0:14.84 98.1% 0+0k 0+0io 0pf+0w