[gmx-users] Nucleotide terminal problems in GORMOS96 force field

Justin Lemkul jalemkul at vt.edu
Fri Oct 12 20:06:04 CEST 2012

On 10/12/12 2:03 PM, gatidaniel wrote:
> I am going to simulate a tRNA molecule using GROMOS96 force field, which
> contain some modified nucleotide.
> I've build the .rtp entry for each modified residues like the this:
> A02-mdf.top <http://gromacs.5086.n6.nabble.com/file/n5001965/A02-mdf.top>
> But pdb2gmx prompt out such error message:
> Fatal error: atom N not found in buiding block 1GUA while combining tdb and
> rtp
> I choose gromos43a1 force field.
> I think pdb2gmx treat my nucleotide as protein, because it cap both terminus
> by NH3+ and COO-.
> So I redo it again, with -ter option, and choose none.
> pdb2gmx say:
> Fatal error: There is a dangling bond at at least one of the terminal ends.
> Select a proper terminal entry.
> Looks like that I should edit the terminal entry, is it correct? My .rtp
> file almost exactly the same as proper nucleotide topology, the differences
> exist only in the residue part.
> Here is another question: why the total charge of single nucleotide molecule
> is -1?

Please note that I answered this post already:


To distill down the essential points, you need to design proper terminal and 
internal nucleotides, and add them to residuetypes.dat.  The process is 
explained here:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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