[gmx-users] Re:gmx-users Digest, Vol 80, Issue 164

gromacs564 gromacs564 at 126.com
Sat Dec 25 11:13:03 CET 2010


Hi  Alan , Oliver
     I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct ,
because all of the [pairs](1-4 interaction) are zero in gromacs top files. I don't know whether this files are correct or not.
     Would you give me some advice? Thank your very much.
  
all the best
xiaodu 
------------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------------
; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333
[ atomtypes ]
;name  bond_type    mass    charge   ptype          sigma      epsilon
HO            HO      0.0000  0.0000  A   0.00000e+00  0.00000e+00
H1            H1      0.0000  0.0000  A   2.47135e-01  6.56888e-02
OS            OS      0.0000  0.0000  A   3.00001e-01  7.11280e-01
CG            CG      0.0000  0.0000  A   3.39967e-01  4.57730e-01
H2            H2      0.0000  0.0000  A   2.29317e-01  6.56888e-02
OH            OH      0.0000  0.0000  A   3.06647e-01  8.80314e-01
[ moleculetype ]
; Name            nrexcl
solute             3
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB
     1         HO      1    ROH    HO1      1    0.44500   1.000000
     2         OH      1    ROH     O1      2   -0.63900  16.000000
     3         CG      2    4GA     C1      3    0.50900  12.000000
     4         H2      2    4GA     H1      4    0.00000   1.000000
     5         CG      2    4GA     C2      5    0.24600  12.000000
     6         H1      2    4GA     H2      6    0.00000   1.000000
     7         OH      2    4GA     O2      7   -0.71300  16.000000
     8         HO      2    4GA    H2O      8    0.43700   1.000000
     9         CG      2    4GA     C3      9    0.28600  12.000000
    10         H1      2    4GA     H3     10    0.00000   1.000000
    11         OH      2    4GA     O3     11   -0.69900  16.000000
    12         HO      2    4GA    H3O     12    0.42700   1.000000
    13         CG      2    4GA     C4     13    0.25400  12.000000
    14         H1      2    4GA     H4     14    0.00000   1.000000
    15         CG      2    4GA     C5     15    0.28300  12.000000
    16         H1      2    4GA     H5     16    0.00000   1.000000
    17         OS      2    4GA     O5     17   -0.57400  16.000000
    18         CG      2    4GA     C6     18    0.27600  12.000000
    19         H1      2    4GA    H61     19    0.00000   1.000000
    20         H1      2    4GA    H62     20    0.00000   1.000000
    21         OH      2    4GA     O6     21   -0.68200  16.000000
    22         HO      2    4GA    H6O     22    0.41800   1.000000
    23         OS      2    4GA     O4     23   -0.46800  16.000000
    24         CG      3    0GA     C1     24    0.50900  12.000000
    25         H2      3    0GA     H1     25    0.00000   1.000000
    26         CG      3    0GA     C2     26    0.24600  12.000000
    27         H1      3    0GA     H2     27    0.00000   1.000000
    28         OH      3    0GA     O2     28   -0.71300  16.000000
    29         HO      3    0GA    H2O     29    0.43700   1.000000
    30         CG      3    0GA     C3     30    0.28600  12.000000
    31         H1      3    0GA     H3     31    0.00000   1.000000
    32         OH      3    0GA     O3     32   -0.69900  16.000000
    33         HO      3    0GA    H3O     33    0.42700   1.000000
    34         CG      3    0GA     C4     34    0.25400  12.000000
    35         H1      3    0GA     H4     35    0.00000   1.000000
    36         OH      3    0GA     O4     36   -0.71000  16.000000
    37         HO      3    0GA    H4O     37    0.43600   1.000000
    38         CG      3    0GA     C5     38    0.28300  12.000000
    39         H1      3    0GA     H5     39    0.00000   1.000000
    40         OS      3    0GA     O5     40   -0.57400  16.000000
    41         CG      3    0GA     C6     41    0.27600  12.000000
    42         H1      3    0GA    H61     42    0.00000   1.000000
    43         H1      3    0GA    H62     43    0.00000   1.000000
    44         OH      3    0GA     O6     44   -0.68200  16.000000
    45         HO      3    0GA    H6O     45    0.41800   1.000000
[ bonds ]
;  ai    aj funct  r  k
    1     2     1  9.6000e-02  4.6275e+05
   21    22     1  9.6000e-02  4.6275e+05
   18    19     1  1.0900e-01  2.8451e+05
   18    20     1  1.0900e-01  2.8451e+05
   15    16     1  1.0900e-01  2.8451e+05
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ pairs ]
;  ai    aj funct
     2      6      1
     1      4      1
     1      5      1
     1     17      1
~~~~~~~~~~~~~~~~~~~~
     5     23      1
     3     11      1
     3     13      1
     3     18      1
    40     44      1
    36     40      1
    36     41      1
    34     44      1
    32     36      1
    32     38      1
    30     40      1
    30     41      1
    28     40      1
    28     32      1
    28     34      1
    26     38      1
    26     36      1
    24     32      1
    24     34      1
    24     41      1
[ angles ]
;  ai    aj    ak funct  theta   cth
    2     3     4     1  1.1000e+02  5.0208e+02
    1     2     3     1  1.0950e+02  4.6024e+02
   23    24    25     1  1.1000e+02  5.0208e+02
   20    18    21     1  1.1000e+02  5.0208e+02
   19    18    20     1  1.0950e+02  3.7656e+02
~~~~~~~~~~~~~~~~~~~
[ dihedrals ]
;i  j   k  l  func C0  ...  C5
    2    3    5    6      3     0.20920     0.62760     0.00000    -0.83680     0.00000     0.00000 ;
    1    2    3    4      3     0.75312     2.25936     0.00000    -3.01248     0.00000     0.00000 ;
    1    2    3    5      3     0.75312     2.25936     0.00000    -3.01248     0.00000     0.00000 ;
~~~~~~~~~~~~~~~~~
[ system ]
45 system
[ molecules ]
; Compound        nmols
solute            1
-------------------------------------------------------------------------------------------------
 
 
 
    

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