Sat Oct 15 12:54:46 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 12:54:46 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: HIR 212 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5774721 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): -42.56600 19.08200 ymin,ymax (A): 5.339000 57.71100 zmin,zma (A): -20.13700 32.59600 x,y,z range (A): 61.64800 52.37200 52.73300 scale (grids/A): 0.5774721 object centre (A): -11.74200 31.52500 6.229500 number of atom coordinates read : 2798 total number of charged atoms : 2710 net assigned charge : 8.514011 assigned positive charge : 417.4491 centred at (gu) : 90.34019 89.39184 89.85139 assigned negative charge : -408.9368 centred at (gu) : 90.27383 89.36455 89.88651 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6829 nv = 96 ne = 84 npr = 50097 no. pairs analyzed = 50097 no. exposed pairs = 4396 no. arc points = 30712 no. surface atoms = 1445 nbur = 1353 mkacc time = 8.0000006E-02 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 = 1.512000 m= 364 mr = 3202 m= 0 mr = 39 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3080 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4347002E-09 1.0110592E-09 midg,1,midg; midg,igrid,midg 1.3647000E-09 1.9203044E-09 1,midg,midg; igrid,midg,midg 4.2627779E-10 3.1689680E-09 gauss-seidel spectral radius is 0.9845365 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 12:54:46 rms-change max change #iterations 9.2120267E-02 14.61418 at 10iterations 6.8842676E-03 1.011631 at 20iterations 6.4544508E-04 0.1062889 at 30iterations 1.2343841E-04 1.5110254E-02 at 40iterations 3.7726386E-05 4.6774298E-03 at 50iterations finished qdiffx linear iterations at : 12:54:49 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.7726386E-05 4.6774298E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 12:54:50 3.487u 0.188s 0:04.00 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 15 2011 at 12:54:50 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: HIR 212 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.732416 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): -42.56600 19.08200 ymin,ymax (A): 5.339000 57.71100 zmin,zma (A): -20.13700 32.59600 x,y,z range (A): 61.64800 52.37200 52.73300 scale (grids/A): 1.732416 object centre (A): -11.74200 31.52500 6.229500 number of atom coordinates read : 2798 total number of charged atoms : 2710 net assigned charge : 8.514011 assigned positive charge : 417.4491 centred at (gu) : 91.01971 88.17471 89.55315 assigned negative charge : -408.9368 centred at (gu) : 90.82139 88.09341 89.65945 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30712 grid for indexing accessible points = 1.400000 m= 26034 mr = 47889 m= 3919 mr = 17573 m= 175 mr = 2137 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 36543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 21102 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) : 0.5774721 object centre at (A) : -11.74200 31.52500 6.229500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0696009E-03 -2.5857615E-03 midg,1,midg; midg,igrid,midg 2.2282416E-02 1.3369129E-02 1,midg,midg; igrid,midg,midg 1.2415815E-02 5.7417634E-03 gauss-seidel spectral radius is 0.9984249 estimated iterations to convergence 200 setup time was (sec) 0.5900000 now iterating at: 12:54:51 rms-change max change #iterations 3.660189 169.0322 at 10iterations 1.614413 58.55936 at 20iterations 0.7108415 26.52081 at 30iterations 0.3143727 11.18811 at 40iterations 0.1389384 5.034961 at 50iterations 6.1286356E-02 2.145716 at 60iterations 2.7202232E-02 0.9916573 at 70iterations 1.2021378E-02 0.4386749 at 80iterations 5.3459229E-03 0.1809521 at 90iterations 2.3896270E-03 8.0896378E-02 at 100iterations 1.0742431E-03 3.5218775E-02 at 110iterations 4.8898114E-04 1.6135216E-02 at 120iterations finished qdiffx linear iterations at : 12:54:59 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 4.8898114E-04 1.6135216E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 12:54:59 8.171u 0.243s 0:09.32 90.2% 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 12:54:59 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: HIR 212 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.598624 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): -42.56600 19.08200 ymin,ymax (A): 5.339000 57.71100 zmin,zma (A): -20.13700 32.59600 x,y,z range (A): 61.64800 52.37200 52.73300 scale (grids/A): 2.598624 object centre (A): -11.74200 31.52500 6.229500 number of atom coordinates read : 2798 total number of charged atoms : 2710 net assigned charge : 8.514011 assigned positive charge : 417.4491 centred at (gu) : 91.52923 87.26170 89.32964 assigned negative charge : -408.9368 centred at (gu) : 91.23203 87.14026 89.48904 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 171399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30712 grid for indexing accessible points = 1.400000 m= 84198 mr = 118145 m= 29860 mr = 64685 m= 6591 mr = 22484 m= 782 mr = 4653 m= 29 mr = 399 m= 0 mr = 8 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 82485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 21669 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) : 1.732416 object centre at (A) : -11.74200 31.52500 6.229500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1035083 -2.9520890E-02 midg,1,midg; midg,igrid,midg 0.3342762 0.1543795 1,midg,midg; igrid,midg,midg 0.2320069 1.5194613E-02 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 1.160000 now iterating at: 12:55:01 rms-change max change #iterations 9.379648 314.9647 at 10iterations 5.589645 153.3050 at 20iterations 3.284011 77.50106 at 30iterations 1.918826 44.66473 at 40iterations 1.116800 25.46992 at 50iterations 0.6463373 15.35508 at 60iterations 0.3730230 8.207375 at 70iterations 0.2144989 4.343102 at 80iterations 0.1231699 2.643753 at 90iterations 7.0409544E-02 1.396687 at 100iterations 4.0268779E-02 0.9094286 at 110iterations 2.3114864E-02 0.4504242 at 120iterations 1.3179175E-02 0.2584763 at 130iterations 7.5081415E-03 0.1686611 at 140iterations 4.2891758E-03 9.3166709E-02 at 150iterations 2.4433867E-03 4.6174049E-02 at 160iterations 1.3941091E-03 2.9878855E-02 at 170iterations 7.9780980E-04 1.6570091E-02 at 180iterations finished qdiffx linear iterations at : 12:55:14 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 7.9780980E-04 1.6570091E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.49000 DelPhi exited at 12:55:15 13.491u 0.333s 0:15.31 90.2% 0+0k 0+0io 0pf+0w