Tue Nov 22 14:10:53 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+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 Tue Nov 22 2011 at 14:10:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 0.6018190 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): -34.67700 13.01900 ymin,ymax (A): 0.3950000 41.11900 zmin,zma (A): -4.4000030E-02 59.11000 x,y,z range (A): 47.69600 40.72400 59.15400 scale (grids/A): 0.6018190 object centre (A): -10.82900 20.75700 29.53300 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 5.000010 assigned positive charge : 285.3821 centred at (gu) : 89.47739 89.74918 89.01643 assigned negative charge : -280.3824 centred at (gu) : 89.37415 89.91185 88.99158 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4744 nv = 96 ne = 84 npr = 39827 no. pairs analyzed = 39827 no. exposed pairs = 2411 no. arc points = 17306 no. surface atoms = 824 nbur = 1122 mkacc time = 8.9999996E-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 = 1.456000 m= 262 mr = 2599 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1786 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5845 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9687942E-09 2.3976996E-09 midg,1,midg; midg,igrid,midg 7.1300024E-09 -2.1927891E-09 1,midg,midg; igrid,midg,midg -7.1922457E-10 4.5616857E-09 gauss-seidel spectral radius is 0.9856554 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 14:11:01 rms-change max change #iterations 9.2063740E-02 15.96804 at 10iterations 7.7781724E-03 1.410053 at 20iterations 6.6565938E-04 0.1172523 at 30iterations 5.6994671E-05 9.9296570E-03 at 40iterations 4.8251727E-06 9.4223022E-04 at 50iterations finished qdiffx linear iterations at : 14:11:09 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 4.8251727E-06 9.4223022E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 14:11:12 3.168u 0.143s 0:15.82 20.8% 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 14:11:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 1.805457 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): -34.67700 13.01900 ymin,ymax (A): 0.3950000 41.11900 zmin,zma (A): -4.4000030E-02 59.11000 x,y,z range (A): 47.69600 40.72400 59.15400 scale (grids/A): 1.805457 object centre (A): -10.82900 20.75700 29.53300 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 5.000010 assigned positive charge : 285.3821 centred at (gu) : 88.43237 89.24777 87.04944 assigned negative charge : -280.3824 centred at (gu) : 88.12280 89.73570 86.97478 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 51584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17306 grid for indexing accessible points = 1.400000 m= 18419 mr = 35260 m= 2605 mr = 13797 m= 120 mr = 1630 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 0.3700000 number of dielectric boundary points 22007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14157 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) : 0.6018190 object centre at (A) : -10.82900 20.75700 29.53300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4708756E-02 2.3397371E-02 midg,1,midg; midg,igrid,midg 1.0816230E-02 -6.0460968E-03 1,midg,midg; igrid,midg,midg -4.2472439E-04 2.8846983E-03 gauss-seidel spectral radius is 0.9984046 estimated iterations to convergence 199 setup time was (sec) 0.6300000 now iterating at: 14:11:20 rms-change max change #iterations 3.183215 172.7649 at 10iterations 1.396462 55.30351 at 20iterations 0.6135656 26.01355 at 30iterations 0.2697200 13.28201 at 40iterations 0.1189303 5.043407 at 50iterations 5.2127305E-02 2.005792 at 60iterations 2.3080977E-02 0.9223070 at 70iterations 1.0113105E-02 0.3786960 at 80iterations 4.4675157E-03 0.1711235 at 90iterations 1.9545124E-03 7.6007843E-02 at 100iterations 8.6531916E-04 3.7872314E-02 at 110iterations 3.8007123E-04 1.4648438E-02 at 120iterations finished qdiffx linear iterations at : 14:11:39 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 3.8007123E-04 1.4648438E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 14:11:42 7.087u 0.204s 0:27.99 26.0% 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 Tue Nov 22 2011 at 14:11:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 2.708185 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): -34.67700 13.01900 ymin,ymax (A): 0.3950000 41.11900 zmin,zma (A): -4.4000030E-02 59.11000 x,y,z range (A): 47.69600 40.72400 59.15400 scale (grids/A): 2.708185 object centre (A): -10.82900 20.75700 29.53300 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 5.000010 assigned positive charge : 285.3821 centred at (gu) : 87.64857 88.87173 85.57418 assigned negative charge : -280.3824 centred at (gu) : 87.18417 89.60365 85.46223 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 119337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17306 grid for indexing accessible points = 1.400000 m= 60057 mr = 85424 m= 21111 mr = 49446 m= 4531 mr = 17329 m= 530 mr = 3369 m= 17 mr = 313 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2113 time to turn everything in is 0.9300000 number of dielectric boundary points 49702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 14527 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) : 1.805457 object centre at (A) : -10.82900 20.75700 29.53300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2727349E-02 0.2152890 midg,1,midg; midg,igrid,midg 8.9834467E-02 -9.3690254E-02 1,midg,midg; igrid,midg,midg -4.1616637E-02 3.4262210E-02 gauss-seidel spectral radius is 0.9991758 estimated iterations to convergence 275 setup time was (sec) 1.230000 now iterating at: 14:11:53 rms-change max change #iterations 7.604970 254.5031 at 10iterations 4.273884 109.5782 at 20iterations 2.398522 52.80885 at 30iterations 1.331942 32.44772 at 40iterations 0.7428888 16.78417 at 50iterations 0.4118707 9.286774 at 60iterations 0.2287684 5.143785 at 70iterations 0.1276386 2.806727 at 80iterations 7.0795216E-02 1.575939 at 90iterations 3.9352152E-02 0.8700705 at 100iterations 2.1890171E-02 0.4599924 at 110iterations 1.2156582E-02 0.2569790 at 120iterations 6.7431238E-03 0.1442795 at 130iterations 3.7499534E-03 7.6543808E-02 at 140iterations 2.0812105E-03 4.5837402E-02 at 150iterations 1.1603433E-03 2.7423859E-02 at 160iterations 6.4379280E-04 1.3637543E-02 at 170iterations 3.5845101E-04 7.4462891E-03 at 180iterations finished qdiffx linear iterations at : 14:12:24 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 3.5845101E-04 7.4462891E-03 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 14:12:26 11.625u 0.222s 0:39.83 29.7% 0+0k 0+0io 0pf+0w