[gmx-users] Special parameters for certain 1-5 LJ pairs (56Acarbo)

[Jon Kapla]

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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