Sun Oct 9 07:41:22 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 Sun Oct 9 2011 at 07:41:22 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1681 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -3.1550 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: 0.7253610 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): 5.487000 48.80400 ymin,ymax (A): 20.17600 69.25500 zmin,zma (A): -6.571000 35.21900 x,y,z range (A): 43.31700 49.07901 41.79000 scale (grids/A): 0.7253610 object centre (A): 27.14550 44.71550 14.32400 number of atom coordinates read : 1681 total number of charged atoms : 1544 net assigned charge : -11.25499 assigned positive charge : 251.3492 centred at (gu) : 90.23997 89.59665 89.26319 assigned negative charge : -262.6041 centred at (gu) : 90.34543 89.51714 89.58018 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5942 nv = 96 ne = 84 npr = 36201 no. pairs analyzed = 36201 no. exposed pairs = 2096 no. arc points = 14734 no. surface atoms = 710 nbur = 971 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 3356 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.2500000 number of dielectric boundary points 2927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1231 ## 88 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2958164E-08 -3.0026686E-07 midg,1,midg; midg,igrid,midg -2.0875520E-07 -8.9222581E-08 1,midg,midg; igrid,midg,midg -7.6889322E-08 -2.1948946E-07 gauss-seidel spectral radius is 0.9900528 estimated iterations to convergence 82 setup time was (sec) 0.4700000 now iterating at: 07:41:23 rms-change max change #iterations 0.2059664 36.09160 at 10iterations 2.6627894E-02 4.443432 at 20iterations 3.4557404E-03 0.4821625 at 30iterations 4.4768816E-04 5.8979034E-02 at 40iterations 5.7567770E-05 8.1577301E-03 at 50iterations finished qdiffx linear iterations at : 07:41:25 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 5.7567770E-05 8.1577301E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 07:41:26 3.176u 0.175s 0:03.62 92.2% 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 Sun Oct 9 2011 at 07:41:26 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1681 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -3.1550 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.176083 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): 5.487000 48.80400 ymin,ymax (A): 20.17600 69.25500 zmin,zma (A): -6.571000 35.21900 x,y,z range (A): 43.31700 49.07901 41.79000 scale (grids/A): 2.176083 object centre (A): 27.14550 44.71550 14.32400 number of atom coordinates read : 1681 total number of charged atoms : 1544 net assigned charge : -11.25499 assigned positive charge : 251.3492 centred at (gu) : 90.72031 88.79003 87.78989 assigned negative charge : -262.6041 centred at (gu) : 91.03643 88.55156 88.74081 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14734 grid for indexing accessible points = 1.400000 m= 25295 mr = 42682 m= 5315 mr = 19686 m= 530 mr = 3847 m= 13 mr = 334 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3286 time to turn everything in is 0.4900000 number of dielectric boundary points 26879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 12305 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) : 0.7253610 object centre at (A) : 27.14550 44.71550 14.32400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1881962E-02 -7.4573845E-02 midg,1,midg; midg,igrid,midg -7.5499170E-02 -1.6428063E-02 1,midg,midg; igrid,midg,midg -3.8051020E-02 -7.2423801E-02 gauss-seidel spectral radius is 0.9988432 estimated iterations to convergence 233 setup time was (sec) 0.7700000 now iterating at: 07:41:27 rms-change max change #iterations 4.440125 261.8941 at 10iterations 2.195842 133.0427 at 20iterations 1.093552 44.45392 at 30iterations 0.5418818 17.92781 at 40iterations 0.2700459 9.924810 at 50iterations 0.1341454 5.300236 at 60iterations 6.6722192E-02 2.212762 at 70iterations 3.3047471E-02 1.074188 at 80iterations 1.6427172E-02 0.5215759 at 90iterations 8.1962533E-03 0.2709265 at 100iterations 4.0686051E-03 0.1239758 at 110iterations 2.0222485E-03 6.6100121E-02 at 120iterations finished qdiffx linear iterations at : 07:41:33 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 2.0222485E-03 6.6100121E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.200000 DelPhi exited at 07:41:33 7.205u 0.162s 0:07.64 96.3% 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 Sun Oct 9 2011 at 07:41:33 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1681 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -3.1550 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: 3.264125 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): 5.487000 48.80400 ymin,ymax (A): 20.17600 69.25500 zmin,zma (A): -6.571000 35.21900 x,y,z range (A): 43.31700 49.07901 41.79000 scale (grids/A): 3.264125 object centre (A): 27.14550 44.71550 14.32400 number of atom coordinates read : 1681 total number of charged atoms : 1544 net assigned charge : -11.25499 assigned positive charge : 251.3492 centred at (gu) : 91.08041 88.18500 86.68491 assigned negative charge : -262.6041 centred at (gu) : 91.55472 87.82735 88.11113 start vw surface at 0.1300000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 143325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14734 grid for indexing accessible points = 1.400000 m= 77129 mr = 103041 m= 33732 mr = 64318 m= 10173 mr = 28745 m= 2043 mr = 8260 m= 304 mr = 1637 m= 25 mr = 222 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 11227 time to turn everything in is 1.480000 number of dielectric boundary points 60494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 12352 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) : 2.176083 object centre at (A) : 27.14550 44.71550 14.32400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2774317 -0.5080169 midg,1,midg; midg,igrid,midg -0.6246008 -0.1056160 1,midg,midg; igrid,midg,midg -0.2454912 -0.5168817 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 1.760000 now iterating at: 07:41:35 rms-change max change #iterations 9.784709 481.5066 at 10iterations 5.660750 214.4561 at 20iterations 3.301246 83.35638 at 30iterations 1.915334 41.03430 at 40iterations 1.110538 23.74154 at 50iterations 0.6459329 12.56525 at 60iterations 0.3754668 7.108601 at 70iterations 0.2182487 4.006712 at 80iterations 0.1267913 2.743774 at 90iterations 7.3516794E-02 1.355827 at 100iterations 4.2683840E-02 0.7832022 at 110iterations 2.4773531E-02 0.4945030 at 120iterations 1.4380259E-02 0.2977228 at 130iterations 8.3581684E-03 0.1517420 at 140iterations 4.8483615E-03 9.1127515E-02 at 150iterations 2.8254488E-03 5.0514221E-02 at 160iterations 1.6410878E-03 3.3194542E-02 at 170iterations 9.4856514E-04 2.1118164E-02 at 180iterations finished qdiffx linear iterations at : 07:41:45 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 9.4856514E-04 2.1118164E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 07:41:45 11.520u 0.249s 0:12.08 97.3% 0+0k 0+0io 0pf+0w