Sat Oct 8 23:56:04 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 8 2011 at 23:56:04 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2454 !!! WARNING: GLM 131 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6321023 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): -13.29500 40.44600 ymin,ymax (A): -31.06600 25.25400 zmin,zma (A): -9.520000 33.47700 x,y,z range (A): 53.74100 56.32000 42.99700 scale (grids/A): 0.6321023 object centre (A): 13.57550 -2.906000 11.97850 number of atom coordinates read : 2454 total number of charged atoms : 2315 net assigned charge : 11.40602 assigned positive charge : 359.3592 centred at (gu) : 89.87703 91.08299 90.53060 assigned negative charge : -347.9539 centred at (gu) : 89.86555 91.07830 90.47052 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6695 nv = 96 ne = 84 npr = 48975 no. pairs analyzed = 48975 no. exposed pairs = 3206 no. arc points = 22990 no. surface atoms = 1078 nbur = 1376 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3505 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2530200E-09 2.0337778E-08 midg,1,midg; midg,igrid,midg 1.0192065E-08 1.7014486E-08 1,midg,midg; igrid,midg,midg 1.2501044E-08 1.3754598E-08 gauss-seidel spectral radius is 0.9870316 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 23:56:05 rms-change max change #iterations 0.1296701 18.31097 at 10iterations 1.2507590E-02 1.741029 at 20iterations 1.3929029E-03 0.2198448 at 30iterations 2.6012384E-04 4.8841476E-02 at 40iterations 8.1031911E-05 1.6721725E-02 at 50iterations finished qdiffx linear iterations at : 23:56:07 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 8.1031911E-05 1.6721725E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 23:56:08 3.126u 0.118s 0:03.53 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 23:56:08 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2454 !!! WARNING: GLM 131 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.896307 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): -13.29500 40.44600 ymin,ymax (A): -31.06600 25.25400 zmin,zma (A): -9.520000 33.47700 x,y,z range (A): 53.74100 56.32000 42.99700 scale (grids/A): 1.896307 object centre (A): 13.57550 -2.906000 11.97850 number of atom coordinates read : 2454 total number of charged atoms : 2315 net assigned charge : 11.40602 assigned positive charge : 359.3592 centred at (gu) : 89.63045 93.24857 91.59129 assigned negative charge : -347.9539 centred at (gu) : 89.59669 93.23489 91.41144 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22990 grid for indexing accessible points = 1.400000 m= 25311 mr = 48439 m= 3969 mr = 18143 m= 232 mr = 2382 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 262 time to turn everything in is 0.5100000 number of dielectric boundary points 32475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 18192 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) : 0.6321023 object centre at (A) : 13.57550 -2.906000 11.97850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4192337E-03 2.2187199E-02 midg,1,midg; midg,igrid,midg 3.4440052E-02 3.1101277E-02 1,midg,midg; igrid,midg,midg 4.2784020E-02 4.7368612E-02 gauss-seidel spectral radius is 0.9986201 estimated iterations to convergence 213 setup time was (sec) 0.7700000 now iterating at: 23:56:09 rms-change max change #iterations 4.010434 171.2620 at 10iterations 1.864387 69.84177 at 20iterations 0.8692368 32.75578 at 30iterations 0.4047772 14.68490 at 40iterations 0.1885614 5.933411 at 50iterations 8.7856837E-02 2.906809 at 60iterations 4.0843107E-02 1.242645 at 70iterations 1.9132473E-02 0.6091080 at 80iterations 8.9692976E-03 0.2949524 at 90iterations 4.2090886E-03 0.1374454 at 100iterations 2.0096265E-03 6.2160492E-02 at 110iterations 9.8187139E-04 3.2020569E-02 at 120iterations finished qdiffx linear iterations at : 23:56:15 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 9.8187139E-04 3.2020569E-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 23:56:15 6.927u 0.149s 0:07.41 95.2% 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 8 2011 at 23:56:15 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2454 !!! WARNING: GLM 131 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.844460 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): -13.29500 40.44600 ymin,ymax (A): -31.06600 25.25400 zmin,zma (A): -9.520000 33.47700 x,y,z range (A): 53.74100 56.32000 42.99700 scale (grids/A): 2.844460 object centre (A): 13.57550 -2.906000 11.97850 number of atom coordinates read : 2454 total number of charged atoms : 2315 net assigned charge : 11.40602 assigned positive charge : 359.3592 centred at (gu) : 89.44552 94.87271 92.38667 assigned negative charge : -347.9539 centred at (gu) : 89.39490 94.85230 92.11723 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 166266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22990 grid for indexing accessible points = 1.400000 m= 81892 mr = 117661 m= 29281 mr = 65507 m= 7012 mr = 23154 m= 996 mr = 5194 m= 54 mr = 619 m= 0 mr = 24 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 996 time to turn everything in is 1.240000 number of dielectric boundary points 73342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 18518 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) : 1.896307 object centre at (A) : 13.57550 -2.906000 11.97850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9117905E-02 0.2213174 midg,1,midg; midg,igrid,midg 0.4965152 0.3672194 1,midg,midg; igrid,midg,midg 0.4020201 0.5213459 gauss-seidel spectral radius is 0.9992593 estimated iterations to convergence 290 setup time was (sec) 1.520000 now iterating at: 23:56:17 rms-change max change #iterations 9.523026 328.2420 at 10iterations 5.619203 131.6421 at 20iterations 3.282139 69.90211 at 30iterations 1.913998 41.15194 at 40iterations 1.113996 22.42328 at 50iterations 0.6458628 12.92787 at 60iterations 0.3740517 7.610243 at 70iterations 0.2160931 4.231693 at 80iterations 0.1250316 2.463865 at 90iterations 7.2041348E-02 1.434349 at 100iterations 4.1645695E-02 0.8009453 at 110iterations 2.4055924E-02 0.4535747 at 120iterations 1.3925471E-02 0.2658997 at 130iterations 8.0831042E-03 0.1638813 at 140iterations 4.7427854E-03 9.9220276E-02 at 150iterations 2.8357594E-03 6.2221527E-02 at 160iterations 1.7450062E-03 4.4305325E-02 at 170iterations 1.1266087E-03 2.9643536E-02 at 180iterations finished qdiffx linear iterations at : 23:56:27 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 1.1266087E-03 2.9643536E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.44000 DelPhi exited at 23:56:27 11.439u 0.168s 0:11.87 97.6% 0+0k 0+0io 0pf+0w