[gmx-users] Error gmx pdb2gro

[Danilo Boskovic]

Edit: the structure is a split_chain generated and exported file from
pymol. It contains only the structure coordinates in format as stated
above, so please TER and END.

On Fri, 21 Jun 2019, 14:14 Danilo Boskovic, <daniloboskovic0095 at gmail.com>
wrote:

> 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
>   C
> ATOM      2  O5'   U B 501      24.120   9.582  -6.276  1.00  5.15
>   O
> ATOM      3  C4'   U B 501      24.186   7.735  -4.679  1.00  4.12
>   C
>
> 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:
>
> http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/tutorial-martini-rna-gmx5
>
>