unanswered Why is the 5'-terminus of MARTINI DNA uncharged?

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1 year 11 months ago - 1 year 11 months ago #9427 by suhas
Hello MARTINI friends,

I have noticed that MARTINI DNA topologies do not contain a charged bead at the 5' end. Is there a reason for this? I am unable to find a justification in the literature.

I have observed this in the DNA strand example on the MARTINI website ( cgmartini.nl/images/applications/dna/dna.itp ), as well as outputs generated by the martinize-dna.py tool accessed from the MARTINI nucleic acids tutorials package ( cgmartini.nl/index.php/force-field-parameters/dna ). I have tinkered with the -nt and -cb flags while running martinize-dna.py and the output topology is unaffected: the 5' end continues to be uncharged. In fact, the -nt and -cb flags do not made any changes to the topology of my single stranded DNA system. Note: the atomistic input files contain charged phasphate groups at the 5' end.

[ atoms ]
1 SN0 1 DT BB2 2 0.0000 45.0000 ; C
2 SC2 1 DT BB3 3 0.0000 45.0000 ; C
3 TN0 1 DT SC1 4 0.0000 45.0000 ; C
4 TT2 1 DT SC2 5 0.0000 45.0000 ; C
5 TT3 1 DT SC3 6 0.0000 45.0000 ; C
6 Q0 2 DG BB1 7 -1.0000 72.0000 ; C
7 SN0 2 DG BB2 8 0.0000 45.0000 ; C
8 SC2 2 DG BB3 9 0.0000 45.0000 ; C
9 TN0 2 DG SC1 10 0.0000 45.0000 ; C
10 TG2 2 DG SC2 11 0.0000 45.0000 ; C
11 TG3 2 DG SC3 12 0.0000 45.0000 ; C
12 TNa 2 DG SC4 13 0.0000 45.0000 ; C


Edit: my atomistic pdb input for DNA was uncharged at the 5' end. I will leave the rest of the question though, to see if there is a reason the 5'- end is uncharged in the example topologies.
Here are the first few lines of the [ atoms ] section from the martinize output itp. Notice how residue 2 (DG) contains a charged Q0 bead, while residue 1 (DT) does not.


Any input would be appreciated.
Thanks!
Last edit: 1 year 11 months ago by suhas. Reason: my atomistic input for DNA was uncharged at the 5' end

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