Hi,

I'm about to simulate a disaccharide in water and have created a topology/ff-mod based on the 56Acarbo parameters based on gromos 53a6 from

"A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers." ?Hansen, H. S.; Hünenberger, P. H. /Journal of computational chemistry/. 2010.
doi: 10.1002/jcc.21675

I'm having troubles understanding how to implement the special 1-5 LJ interactions (N2 and N5, p 1008 in the article) used in that paper. I tried to use the [ pairs_nb ] section in the molecule topology since I believe the [ pairs ] section is for 1-4 interactions only, but with that grompp failed with the following error:

Fatal error:
Invalid case in switch statement, file topio.c, line 905
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

This error seems to disappear when the section is commented out.

Thus I have a couple of questions that someone might be able to answer:

Can I use the [ pairs ] section for 1-5 interactions,
or do you have any other suggestions (I'm modifying a copy of gromos53a6.ff/)?
What is the [ pairs_nb ] used for?

Below follows a relevant section of my molecule.itp, the charges are there because that is how pairs_nb looks in the manual. The variables N1-N5 are defined in the ffbonded.itp file.

[ pairs ]
;  ai    aj funct
    1     4     1
    1    12     1
    1    14     1
    2     5     1
    2    11     1
    2    13     1
    3     6     1
    3    12     1
    4    13     1
    5     8     1
    6    11     1
    6    15     1
    6    19     1
    7     8     1
    7    10     1
    8     9     1
   10    25     1
   14    17     1
   14    24     1
   14    26     1
   15    18     1
   15    27     1
   16    19     1
   16    26     1
   17    27     1
   18    21     1
   18    24     1
   18    25     1
   20    21     1
   20    25     1
   21    22     1
   23    25     1
    9     6     1  N3 ;C6 C1
    9     2     1  N3 ;C6 C3
   22    15     1  N3 ;C12 C8
   22    19     1  N3 ;C12 C11
   25     2     1  N4 ;O9 C3
   25     4     1  N4 ;O9 C5
   10     3     1  N4 ;O2 C4
    7     6     1  N4 ;O3 C1
    7     4     1  N4 ;O3 C5
    8     1     1  N4 ;O4 C2
   25    16     1  N4 ;O9 C9
   23    15     1  N4 ;O1 C8
   23    17     1  N4 ;O1 C10
   20    17     1  N4 ;O7 C10
   20    19     1  N4 ;O7 C11
   21    14     1  N4 ;O8 C7

[ pairs_nb ]
   11     3     1    0.42    0.232    N2 ;HO2 C4
   11     5     1    0.42   -0.464    N2 ;HO2 O5
   12     6     1    0.42    0.464    N2 ;HO3 C1
   12     4     1    0.42    0.232    N2 ;HO3 C5
   13     1     1    0.42    0.232    N2 ;HO4 C2
   13     5     1    0.42   -0.464    N2 ;HO4 O5
   26    19     1    0.42    0.464    N2 ;H11 C11
   26    17     1    0.42    0.232    N2 ;H11 C10
   27    14     1    0.42    0.232    N2 ;H12 C7
   27    18     1    0.42   -0.464    N2 ;H12 O6
   25     9     1   -0.464   0        N5 ;O9 C6
    7     9     1   -0.642   0        N5 ;O3 C6
   23    22     1   -0.464   0        N5 ;O1 C12
   20    22     1   -0.642   0        N5 ;O7 C12

Thanks in advance!

Regards
Jon
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