[gmx-users] Error gmx pdb2gro

Danilo Boskovic daniloboskovic0095 at gmail.com
Fri Jun 21 14:14:23 CEST 2019

I am trying to backmap an RNA file from the MARTINI tutorial as stated in
the tutorial but i am getting error atom N not found in buiding block while
combining tdb and rtp when trying to generate a topology file. Im using
Gromacs 2018.7. It also says

Start terminus U-501: NH3+
End terminus A-511: COO-

for an RNA.

Example first three lines of PDB file:

ATOM      1  C5'   U B 501      23.332   8.576  -5.633  1.00  4.88
ATOM      2  O5'   U B 501      24.120   9.582  -6.276  1.00  5.15
ATOM      3  C4'   U B 501      24.186   7.735  -4.679  1.00  4.12

It seems that the format of the PDB is recognized as a protein. I am using
CHARMM and tip3p. I have a tip3p.itp file, tried to use #include but it did
not help. For full tutorial:

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