[gmx-users] gmx anadock

Hello When I put pdb file from gmx cluster in gmx anadock, gromacs gave error that it cannot find  pdb files while my cluster pdb file involve 40 pdbs in one file. I was wondering if you could give me some advice. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] 5' phosphate of RNA

Thank you Justin I saw SOMNATH question and your answer about 5' PHO on 5 Jul. According that answer,  I  put PRES 5 PHO from  top_all36_na.rtf   file in merged.n.tdb  file after [5TER] section but I receive many errors like: Atom NA not found in  1GUN buiding block wile rtp and itp Atom N not

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

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