[gmx-users] Error gmx pdb2gro
daniloboskovic0095 at gmail.com
Sat Jun 22 00:35:18 CEST 2019
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
> > 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
> > CHARMM and tip3p. I have a tip3p.itp file, tried to use #include but it
> > not help. For full tutorial:
> 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 A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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