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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