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
--
========================================
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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