[gmx-users] Error gmx pdb2gro

[Justin Lemkul]

On 6/21/19 8:14 AM, Danilo Boskovic 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

You have to manually choose termini with CHARMM36. This is because there 
is no way to split proteins, nucleic acids, etc. into their own files 
automatically when reading in the whole force field and we try to avoid 
hard-coding as much as we possibly can.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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