[gmx-users] Error gmx pdb2gro

[Danilo Boskovic]

OK. And could you explain how? I just started to learn doing simulations
and am an undergraduate. Can't find any documentation on what you said I
need to do.

On Fri, 21 Jun 2019, 16:11 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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