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

[Justin Lemkul]

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:

http://lists.gromacs.org/pipermail/gmx-users/2012-October/075409.html

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:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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