Sat Oct 8 13:29:57 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+sph.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 = amb.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 13:29:57 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6205659 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): -11.22000 44.70400 ymin,ymax (A): 10.67200 55.15800 zmin,zma (A): 37.16300 94.53000 x,y,z range (A): 55.92400 44.48600 57.36700 scale (grids/A): 0.6205659 object centre (A): 16.74200 32.91500 65.84650 number of atom coordinates read : 3001 total number of charged atoms : 2855 net assigned charge : -0.9999939 assigned positive charge : 448.6916 centred at (gu) : 88.92373 89.53597 91.33700 assigned negative charge : -449.6924 centred at (gu) : 88.86959 89.45715 91.25037 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7743 nv = 96 ne = 84 npr = 61998 no. pairs analyzed = 61998 no. exposed pairs = 3511 no. arc points = 24161 no. surface atoms = 1209 nbur = 1792 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 4486 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2399 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9562 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6939045E-09 7.9571212E-09 midg,1,midg; midg,igrid,midg -7.8046813E-09 4.7463220E-09 1,midg,midg; igrid,midg,midg -6.4647452E-09 2.6447122E-09 gauss-seidel spectral radius is 0.9865835 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 13:29:58 rms-change max change #iterations 0.1385074 17.93096 at 10iterations 1.3051495E-02 1.774509 at 20iterations 1.3158735E-03 0.1790638 at 30iterations 1.7593178E-04 2.4032593E-02 at 40iterations 3.5855741E-05 5.2089691E-03 at 50iterations finished qdiffx linear iterations at : 13:30:01 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 3.5855741E-05 5.2089691E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 13:30:01 3.196u 0.169s 0:03.66 91.5% 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 Sat Oct 8 2011 at 13:30:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.861698 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): -11.22000 44.70400 ymin,ymax (A): 10.67200 55.15800 zmin,zma (A): 37.16300 94.53000 x,y,z range (A): 55.92400 44.48600 57.36700 scale (grids/A): 1.861698 object centre (A): 16.74200 32.91500 65.84650 number of atom coordinates read : 3001 total number of charged atoms : 2855 net assigned charge : -0.9999939 assigned positive charge : 448.6916 centred at (gu) : 86.77071 88.60738 94.01069 assigned negative charge : -449.6924 centred at (gu) : 86.60861 88.37129 93.75092 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24161 grid for indexing accessible points = 1.400000 m= 31171 mr = 61389 m= 4487 mr = 23394 m= 210 mr = 2697 m= 4 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 33181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22428 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) : 0.6205659 object centre at (A) : 16.74200 32.91500 65.84650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9738575E-02 1.5416570E-02 midg,1,midg; midg,igrid,midg -3.6614528E-03 1.1549947E-02 1,midg,midg; igrid,midg,midg -4.7369476E-02 7.4163699E-03 gauss-seidel spectral radius is 0.9986095 estimated iterations to convergence 213 setup time was (sec) 0.8400000 now iterating at: 13:30:02 rms-change max change #iterations 4.428390 188.1587 at 10iterations 2.057036 66.55766 at 20iterations 0.9635792 29.30769 at 30iterations 0.4477320 14.04443 at 40iterations 0.2089218 6.150212 at 50iterations 9.7421870E-02 3.006202 at 60iterations 4.5381021E-02 1.395691 at 70iterations 2.1155149E-02 0.5804367 at 80iterations 9.8876692E-03 0.3115883 at 90iterations 4.6406966E-03 0.1349220 at 100iterations 2.1745306E-03 6.8916321E-02 at 110iterations 1.0298013E-03 3.6883354E-02 at 120iterations finished qdiffx linear iterations at : 13:30:08 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 1.0298013E-03 3.6883354E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 13:30:08 6.918u 0.169s 0:07.36 96.0% 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 Sat Oct 8 2011 at 13:30:09 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.792547 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): -11.22000 44.70400 ymin,ymax (A): 10.67200 55.15800 zmin,zma (A): 37.16300 94.53000 x,y,z range (A): 55.92400 44.48600 57.36700 scale (grids/A): 2.792547 object centre (A): 16.74200 32.91500 65.84650 number of atom coordinates read : 3001 total number of charged atoms : 2855 net assigned charge : -0.9999939 assigned positive charge : 448.6916 centred at (gu) : 85.15585 87.91084 96.01575 assigned negative charge : -449.6924 centred at (gu) : 84.91284 87.55701 95.62625 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 196706 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24161 grid for indexing accessible points = 1.400000 m= 101706 mr = 148148 m= 35781 mr = 84685 m= 7798 mr = 28961 m= 934 mr = 5692 m= 36 mr = 553 m= 0 mr = 1 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 74921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 22834 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) : 1.861698 object centre at (A) : 16.74200 32.91500 65.84650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6204404E-02 0.1830008 midg,1,midg; midg,igrid,midg -2.3870170E-02 0.1218225 1,midg,midg; igrid,midg,midg -0.6353666 0.1667483 gauss-seidel spectral radius is 0.9992563 estimated iterations to convergence 289 setup time was (sec) 1.700000 now iterating at: 13:30:10 rms-change max change #iterations 10.46486 317.6414 at 10iterations 6.132781 148.8465 at 20iterations 3.558495 94.26468 at 30iterations 2.064900 41.78063 at 40iterations 1.195625 21.76762 at 50iterations 0.6891315 13.68046 at 60iterations 0.3969015 7.153380 at 70iterations 0.2288629 4.574516 at 80iterations 0.1317447 2.350619 at 90iterations 7.6069325E-02 1.335660 at 100iterations 4.3731064E-02 0.7354317 at 110iterations 2.5118690E-02 0.4294462 at 120iterations 1.4447848E-02 0.2735615 at 130iterations 8.3269821E-03 0.1453056 at 140iterations 4.8046438E-03 8.6387634E-02 at 150iterations 2.7814351E-03 4.6485901E-02 at 160iterations 1.6152886E-03 2.8900623E-02 at 170iterations 9.4609614E-04 1.7715454E-02 at 180iterations finished qdiffx linear iterations at : 13:30:20 total time elapsed so far: 11.25000 # loops : 180 mean,max change (kT/e) : 9.4609614E-04 1.7715454E-02 energy calculations done at 11.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 13:30:21 11.428u 0.178s 0:11.96 96.9% 0+0k 0+0io 0pf+0w