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