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

Justin Lemkul jalemkul at vt.edu
Tue Oct 9 15:03:06 CEST 2012

On 10/9/12 3:34 AM, 史卜吉 wrote:
>   I am going to simulate a tRNA molecule using GROMOS96 force field, which
> contain some modified nucleotide.

Gromos96 parameters are rather poor for nucleotides.  AMBER or CHARMM parameter 
sets are far better suited for simulations of nucleic acids.

> I've build the .rtp entry for each modified residues like
> this<https://docs.google.com/document/d/13t-stSQjlVMPUJqm5JCy-qtvXnHqC85xvS3fheHx0oE/edit>
> .
> 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.

The Gromos96 43A1 parameter set does not have entries for 5' and 3' nucleotides, 
so that's probably the root of the problem.  There is a slight error in 
residuetypes.dat, such that the residue names used by 43A1 are not identified as 
being DNA/RNA.  That should probably be fixed, but it will not solve your issue.

> Here is another question: why the total charge of single nucleotide
> molecule is -1?

The phosphate group of a nucleotide has a -1 charge.



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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