DNA and RNA phosphate termini

User discussions
1

GROMACS version:2020.1
GROMACS modification: Yes/No
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Hi All
All of the available ff does not consider the phosphate termini of DNA and RNA

I have tried many amber ff and charm ff but GROMACS keeps giving me fatal error because of no phosphate group at rtp entry. Deleting the phosphate group will solve the problem. Do you have any idea of the consequences of doing so?

adding -ter or nochargegrp might solve the problem . Any suggestions?
I was thinking to parameterize the ff and add a .tdb entry to consider the phosphate group but unfortunately, I don’t know how to do that

if there are any refined ff you recommend or any useful links or tutorials please let me know

Thank you All

2

Hi,

Both CHARMM and AMBER force field has 3’- and 5’ termini. To apply them you have to use in pdb2gmx the option -ter . Those are the standard termini for RNA and DNA simulations.

If you are interested to have an extra phosphate group at the 5’ termini or 3’ termini (very unusual and also problematic concerning the protonation PO4H- or PO4?), you can create a new entry in the *.n.tdb and *.c.tdb file with the appropriate atomic charges.
All the parameters are already available in both force field, you need just to redistribute the charges among the PO4 or PO4H group.

Kind regards