Wed Dec 28 11:01:12 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 Wed Dec 28 2011 at 11:01:12 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 0.6226497 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): -35.24000 10.57100 ymin,ymax (A): 0.3200001 41.47600 zmin,zma (A): -0.6670000 56.50800 x,y,z range (A): 45.81100 41.15600 57.17500 scale (grids/A): 0.6226497 object centre (A): -12.33450 20.89800 27.92050 number of atom coordinates read : 1970 total number of charged atoms : 1770 net assigned charge : -21.95202 assigned positive charge : 263.9225 centred at (gu) : 90.23660 89.81210 90.00676 assigned negative charge : -285.8742 centred at (gu) : 90.13001 89.99841 89.99147 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5212 nv = 96 ne = 84 npr = 40222 no. pairs analyzed = 40222 no. exposed pairs = 2473 no. arc points = 17128 no. surface atoms = 843 nbur = 1127 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 264 mr = 2863 m= 1 mr = 53 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 0.3000000 number of dielectric boundary points 2561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1675 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9968450E-08 -1.8405784E-08 midg,1,midg; midg,igrid,midg -9.8991197E-09 -2.8088930E-08 1,midg,midg; igrid,midg,midg -2.3662045E-08 -1.4300165E-08 gauss-seidel spectral radius is 0.9865875 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 11:01:13 rms-change max change #iterations 0.1142103 22.43069 at 10iterations 1.0611217E-02 1.711891 at 20iterations 9.6983282E-04 0.1594620 at 30iterations 8.9835477E-05 1.2348175E-02 at 40iterations 8.4045387E-06 1.4076233E-03 at 50iterations finished qdiffx linear iterations at : 11:01:17 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 8.4045387E-06 1.4076233E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 11:01:17 4.609u 0.279s 0:05.45 89.3% 0+0k 0+0io 6pf+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 Wed Dec 28 2011 at 11:01:17 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 1.867949 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): -35.24000 10.57100 ymin,ymax (A): 0.3200001 41.47600 zmin,zma (A): -0.6670000 56.50800 x,y,z range (A): 45.81100 41.15600 57.17500 scale (grids/A): 1.867949 object centre (A): -12.33450 20.89800 27.92050 number of atom coordinates read : 1970 total number of charged atoms : 1770 net assigned charge : -21.95202 assigned positive charge : 263.9225 centred at (gu) : 90.71001 89.43663 90.02045 assigned negative charge : -285.8742 centred at (gu) : 90.39041 89.99548 89.97468 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 56245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17128 grid for indexing accessible points = 1.400000 m= 20811 mr = 38806 m= 3144 mr = 15761 m= 183 mr = 1992 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 171 time to turn everything in is 0.5500000 number of dielectric boundary points 23754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13931 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) : 0.6226497 object centre at (A) : -12.33450 20.89800 27.92050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4442987E-02 -5.5713434E-02 midg,1,midg; midg,igrid,midg -1.5002354E-02 -4.2156294E-02 1,midg,midg; igrid,midg,midg -2.7114607E-02 -3.0688157E-02 gauss-seidel spectral radius is 0.9985073 estimated iterations to convergence 205 setup time was (sec) 0.8800000 now iterating at: 11:01:19 rms-change max change #iterations 3.384387 161.9030 at 10iterations 1.536700 55.32230 at 20iterations 0.6923090 23.82330 at 30iterations 0.3132733 11.30810 at 40iterations 0.1415552 5.660187 at 50iterations 6.4214170E-02 2.347054 at 60iterations 2.8921736E-02 1.016726 at 70iterations 1.3079597E-02 0.5123444 at 80iterations 5.9282840E-03 0.2097015 at 90iterations 2.6816344E-03 9.3036175E-02 at 100iterations 1.2146155E-03 4.4483185E-02 at 110iterations 5.4866693E-04 2.0076752E-02 at 120iterations finished qdiffx linear iterations at : 11:01:30 total time elapsed so far: 12.12000 # loops : 120 mean,max change (kT/e) : 5.4866693E-04 2.0076752E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 11:01:31 12.314u 0.468s 0:13.26 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 Wed Dec 28 2011 at 11:01:31 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 2.801924 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): -35.24000 10.57100 ymin,ymax (A): 0.3200001 41.47600 zmin,zma (A): -0.6670000 56.50800 x,y,z range (A): 45.81100 41.15600 57.17500 scale (grids/A): 2.801924 object centre (A): -12.33450 20.89800 27.92050 number of atom coordinates read : 1970 total number of charged atoms : 1770 net assigned charge : -21.95202 assigned positive charge : 263.9225 centred at (gu) : 91.06508 89.15512 90.03086 assigned negative charge : -285.8742 centred at (gu) : 90.58556 89.99329 89.96208 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 129745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17128 grid for indexing accessible points = 1.400000 m= 66987 mr = 93715 m= 24611 mr = 55378 m= 5644 mr = 20236 m= 739 mr = 4369 m= 58 mr = 516 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 1.330000 number of dielectric boundary points 53546 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 14160 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) : 1.867949 object centre at (A) : -12.33450 20.89800 27.92050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8055577 -0.8380706 midg,1,midg; midg,igrid,midg -0.1661140 -0.4536588 1,midg,midg; igrid,midg,midg -0.2826076 -0.3290757 gauss-seidel spectral radius is 0.9992056 estimated iterations to convergence 280 setup time was (sec) 1.650000 now iterating at: 11:01:33 rms-change max change #iterations 8.005426 326.9706 at 10iterations 4.580962 152.5983 at 20iterations 2.585361 62.99831 at 30iterations 1.460733 33.58928 at 40iterations 0.8230193 18.73561 at 50iterations 0.4638458 10.17638 at 60iterations 0.2610672 5.670166 at 70iterations 0.1469905 3.309570 at 80iterations 8.2530513E-02 1.738373 at 90iterations 4.6443533E-02 0.9725409 at 100iterations 2.6118413E-02 0.5273962 at 110iterations 1.4687464E-02 0.3486328 at 120iterations 8.2610976E-03 0.1691283 at 130iterations 4.6334118E-03 9.5703125E-02 at 140iterations 2.6102425E-03 5.4393291E-02 at 150iterations 1.4679437E-03 3.1051636E-02 at 160iterations 8.2412647E-04 1.7021179E-02 at 170iterations 4.6199429E-04 1.0379791E-02 at 180iterations finished qdiffx linear iterations at : 11:01:50 total time elapsed so far: 19.25000 # loops : 180 mean,max change (kT/e) : 4.6199429E-04 1.0379791E-02 energy calculations done at 19.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.43000 DelPhi exited at 11:01:51 19.436u 0.501s 0:20.43 97.5% 0+0k 0+0io 0pf+0w