[gmx-users] amb2gmx.pl file

Oliver Grant olymacfoogal at gmail.com
Sun Dec 26 17:16:56 CET 2010


Hi Xiaodu,

The fudgeLJ under defaults should be 1.0 for GLYCAM. I'm unable to check my
own files right now so can't compare. When you run grompp check in the
output that fudge is set to 1.0. So there will be no protein in your
simulation correct? I think there is a way to do mixed scaling in gromacs
but I haven't looked into it.

Oliver

2010/12/25 gromacs564 <gromacs564 at 126.com>

> 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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>
>
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>
>
> --
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