Sun Oct 9 07:40:58 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+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 Sun Oct 9 2011 at 07:40:58 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: 284 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: 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 : 249.7492 centred at (gu) : 90.23395 89.61141 89.26096 assigned negative charge : -261.0041 centred at (gu) : 90.33199 89.53267 89.57330 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 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 = 7.9999998E-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 = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.2200000 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 0.3300000 number of grid points assigned charge 6413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8552209E-08 -2.9648885E-07 midg,1,midg; midg,igrid,midg -2.0736613E-07 -9.0174240E-08 1,midg,midg; igrid,midg,midg -8.1608050E-08 -2.1400275E-07 gauss-seidel spectral radius is 0.9900528 estimated iterations to convergence 82 setup time was (sec) 0.4600000 now iterating at: 07:40:59 rms-change max change #iterations 0.2034009 36.64585 at 10iterations 2.6255244E-02 4.206249 at 20iterations 3.4160763E-03 0.4726896 at 30iterations 4.4248003E-04 5.8952332E-02 at 40iterations 5.6800134E-05 8.0337524E-03 at 50iterations finished qdiffx linear iterations at : 07:41:02 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 5.6800134E-05 8.0337524E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 07:41:02 3.581u 0.149s 0:04.01 92.7% 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 07:41:02 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: 284 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: 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 : 249.7492 centred at (gu) : 90.70222 88.83426 87.78318 assigned negative charge : -261.0041 centred at (gu) : 90.99609 88.59814 88.72018 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 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 = 0.2800000 no. cavity mid-points inaccessible to solvent = 3286 time to turn everything in is 0.5700000 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 0.6900000 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 2.0596076E-02 -7.3528856E-02 midg,1,midg; midg,igrid,midg -7.5366944E-02 -1.6594393E-02 1,midg,midg; igrid,midg,midg -3.9388299E-02 -7.0912160E-02 gauss-seidel spectral radius is 0.9988432 estimated iterations to convergence 233 setup time was (sec) 0.8500000 now iterating at: 07:41:03 rms-change max change #iterations 4.402080 261.8942 at 10iterations 2.178464 133.0427 at 20iterations 1.084414 44.45563 at 30iterations 0.5373427 18.16873 at 40iterations 0.2678471 9.478003 at 50iterations 0.1330697 5.160984 at 60iterations 6.6199645E-02 2.177492 at 70iterations 3.2784361E-02 1.059113 at 80iterations 1.6297296E-02 0.5191364 at 90iterations 8.1299366E-03 0.2707605 at 100iterations 4.0354864E-03 0.1228390 at 110iterations 2.0061431E-03 6.6279411E-02 at 120iterations finished qdiffx linear iterations at : 07:41:09 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 2.0061431E-03 6.6279411E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 07:41:10 7.130u 0.193s 0:07.62 96.0% 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 Sun Oct 9 2011 at 07:41:10 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: 284 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: 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 : 249.7492 centred at (gu) : 91.05328 88.25139 86.67482 assigned negative charge : -261.0041 centred at (gu) : 91.49423 87.89723 88.08020 start vw surface at 0.1200000 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 = 0.6700001 no. cavity mid-points inaccessible to solvent = 11227 time to turn everything in is 1.460000 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 1.570000 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 0.2666650 -0.4998336 midg,1,midg; midg,igrid,midg -0.6238417 -0.1067417 1,midg,midg; igrid,midg,midg -0.2572505 -0.5035604 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 1.730000 now iterating at: 07:41:12 rms-change max change #iterations 9.711847 481.5065 at 10iterations 5.616848 214.4561 at 20iterations 3.275371 83.35605 at 30iterations 1.900412 41.03406 at 40iterations 1.102121 23.83329 at 50iterations 0.6409299 12.57268 at 60iterations 0.3725981 6.963478 at 70iterations 0.2166786 4.004893 at 80iterations 0.1258663 2.739380 at 90iterations 7.2985105E-02 1.323029 at 100iterations 4.2362280E-02 0.7662201 at 110iterations 2.4588123E-02 0.4865494 at 120iterations 1.4272613E-02 0.2969227 at 130iterations 8.2967356E-03 0.1512823 at 140iterations 4.8135072E-03 9.0741873E-02 at 150iterations 2.8045042E-03 5.1033020E-02 at 160iterations 1.6291883E-03 3.2593727E-02 at 170iterations 9.4158575E-04 2.0751953E-02 at 180iterations finished qdiffx linear iterations at : 07:41:21 total time elapsed so far: 11.04000 # loops : 180 mean,max change (kT/e) : 9.4158575E-04 2.0751953E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 07:41:22 11.215u 0.192s 0:11.68 97.6% 0+0k 0+0io 0pf+0w