[gmx-users] Error gmx pdb2gro
jalemkul at vt.edu
Fri Jun 21 16:10:51 CEST 2019
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
> 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:
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.
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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