Tue Oct 11 06:40:03 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 Tue Oct 11 2011 at 06:40:03 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2029 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7131124 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): -20.38800 24.73700 ymin,ymax (A): -28.56400 11.19800 zmin,zma (A): -13.32500 36.59700 x,y,z range (A): 45.12500 39.76200 49.92200 scale (grids/A): 0.7131124 object centre (A): 2.174500 -8.683001 11.63600 number of atom coordinates read : 2029 total number of charged atoms : 1895 net assigned charge : 6.931010 assigned positive charge : 306.7821 centred at (gu) : 90.00836 90.46118 89.52365 assigned negative charge : -299.8511 centred at (gu) : 89.82465 90.42795 89.50015 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7031 nv = 96 ne = 84 npr = 40963 no. pairs analyzed = 40963 no. exposed pairs = 2439 no. arc points = 16838 no. surface atoms = 831 nbur = 1198 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4026 m= 2 mr = 72 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 0.2500000 number of dielectric boundary points 3385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1536 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7658 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9140678E-08 7.2692842E-08 midg,1,midg; midg,igrid,midg 4.4968733E-08 9.2450072E-08 1,midg,midg; igrid,midg,midg -3.3887591E-08 1.6433785E-07 gauss-seidel spectral radius is 0.9897430 estimated iterations to convergence 80 setup time was (sec) 0.5100000 now iterating at: 06:40:04 rms-change max change #iterations 0.2028938 30.89011 at 10iterations 2.5910107E-02 3.484623 at 20iterations 3.5555239E-03 0.4716110 at 30iterations 5.7535758E-04 6.9831848E-02 at 40iterations 1.3088956E-04 1.4099121E-02 at 50iterations finished qdiffx linear iterations at : 06:40:08 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 1.3088956E-04 1.4099121E-02 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 06:40:08 4.347u 0.403s 0:05.06 93.6% 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 Oct 11 2011 at 06:40:08 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2029 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.139337 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): -20.38800 24.73700 ymin,ymax (A): -28.56400 11.19800 zmin,zma (A): -13.32500 36.59700 x,y,z range (A): 45.12500 39.76200 49.92200 scale (grids/A): 2.139337 object centre (A): 2.174500 -8.683001 11.63600 number of atom coordinates read : 2029 total number of charged atoms : 1895 net assigned charge : 6.931010 assigned positive charge : 306.7821 centred at (gu) : 90.02500 91.38364 88.57098 assigned negative charge : -299.8511 centred at (gu) : 89.47390 91.28411 88.50048 start vw surface at 0.1000000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16838 grid for indexing accessible points = 1.400000 m= 29448 mr = 52846 m= 5807 mr = 22231 m= 563 mr = 3884 m= 15 mr = 276 m= 0 mr = 5 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 30980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15052 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) : 0.7131124 object centre at (A) : 2.174500 -8.683001 11.63600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1504494E-02 4.2169273E-02 midg,1,midg; midg,igrid,midg 3.5469627E-03 3.6505572E-02 1,midg,midg; igrid,midg,midg 1.8416202E-02 4.1173406E-02 gauss-seidel spectral radius is 0.9988428 estimated iterations to convergence 233 setup time was (sec) 0.9800000 now iterating at: 06:40:10 rms-change max change #iterations 4.596446 222.5322 at 10iterations 2.280346 82.84555 at 20iterations 1.138084 35.26090 at 30iterations 0.5666968 17.53137 at 40iterations 0.2831794 10.17625 at 50iterations 0.1413214 4.351999 at 60iterations 7.0398837E-02 2.264736 at 70iterations 3.5252415E-02 1.174313 at 80iterations 1.7724367E-02 0.5494976 at 90iterations 8.9415601E-03 0.3062420 at 100iterations 4.5192884E-03 0.1328654 at 110iterations 2.3252016E-03 7.8113556E-02 at 120iterations finished qdiffx linear iterations at : 06:40:20 total time elapsed so far: 11.37000 # loops : 120 mean,max change (kT/e) : 2.3252016E-03 7.8113556E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.53000 DelPhi exited at 06:40:21 11.535u 0.454s 0:12.37 96.8% 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 Oct 11 2011 at 06:40:21 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2029 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.209006 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): -20.38800 24.73700 ymin,ymax (A): -28.56400 11.19800 zmin,zma (A): -13.32500 36.59700 x,y,z range (A): 45.12500 39.76200 49.92200 scale (grids/A): 3.209006 object centre (A): 2.174500 -8.683001 11.63600 number of atom coordinates read : 2029 total number of charged atoms : 1895 net assigned charge : 6.931010 assigned positive charge : 306.7821 centred at (gu) : 90.03763 92.07552 87.85649 assigned negative charge : -299.8511 centred at (gu) : 89.21094 91.92615 87.75070 start vw surface at 0.1000000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 171517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16838 grid for indexing accessible points = 1.400000 m= 91932 mr = 127234 m= 37450 mr = 76343 m= 11101 mr = 30715 m= 2246 mr = 8647 m= 284 mr = 1604 m= 13 mr = 184 m= 0 mr = 12 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 69804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 15160 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) : 2.139337 object centre at (A) : 2.174500 -8.683001 11.63600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6566580 0.3377185 midg,1,midg; midg,igrid,midg 2.5778827E-03 0.2825375 1,midg,midg; igrid,midg,midg 0.3037933 0.3091829 gauss-seidel spectral radius is 0.9992954 estimated iterations to convergence 297 setup time was (sec) 2.240000 now iterating at: 06:40:23 rms-change max change #iterations 10.16467 393.4902 at 10iterations 6.009906 121.8491 at 20iterations 3.547654 76.10544 at 30iterations 2.088190 43.12795 at 40iterations 1.227212 22.95947 at 50iterations 0.7222012 12.97575 at 60iterations 0.4236190 8.211651 at 70iterations 0.2481373 4.637513 at 80iterations 0.1454272 2.499704 at 90iterations 8.5311577E-02 1.463295 at 100iterations 5.0184019E-02 0.9217577 at 110iterations 2.9671242E-02 0.5935850 at 120iterations 1.7706923E-02 0.3204803 at 130iterations 1.0739416E-02 0.1917925 at 140iterations 6.7280815E-03 0.1248627 at 150iterations 4.3869722E-03 8.9485168E-02 at 160iterations 3.0289111E-03 5.9816360E-02 at 170iterations 2.2096108E-03 4.2861938E-02 at 180iterations finished qdiffx linear iterations at : 06:40:39 total time elapsed so far: 17.99000 # loops : 180 mean,max change (kT/e) : 2.2096108E-03 4.2861938E-02 energy calculations done at 17.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.15000 DelPhi exited at 06:40:40 18.157u 0.473s 0:19.06 97.6% 0+0k 0+0io 0pf+0w