[gmx-users] phosphate atoms on 5' Of RNA

[mohammad fathabadi]

Dear Users 
I has a RNA that has phosphate atoms (P,OP1,OP2,OP3) on 5'.Most RNA and DNA have phosphate atoms on 3'  not on 5' and for this all force fields don't know phosphate atoms on 5' of RNA.
pdb2gmx make  errors like: OP3 atom isn't  on rtp file .If I delete phosphate atoms from 5' of RNA , I don't have any problem.How can I solve this problem without deleting 5' phosphate atoms.regards