AMBER Archive (2004)

Subject: RE: AMBER: contributed parameters (modified base - PSU)

From: S. Frank Yan (
Date: Tue Feb 17 2004 - 20:32:56 CST

> If one would like to generate his or her own RESP charges for
> pseudouridine or any modified nucleotide using Amber 7. How would one
> about it? Any suggestion
> will be appreciated.

A useful procedure to generate RESP charges for any modified nucleotides
1. Obtain the conformation of the modified nucleotides (pay special
attention to the sugar pucker, since this may affect the resultant
charges). Preferably, you should get several different conformations of
the modified nucleotides you wish to simulate and compute the charges
for each of them.
2. Compute the electrostatic potentials of the modified nucleotides
using Gaussian with 6-31G* basis set (this may take several hours
depending on the machine you use)
3. Use the RESP module in AMBER package to compute the RESP charges of
the modified residue. In many cases, you may want to "equivalent" the
charges on some atoms, say the three hydrogen atoms of a methyl group
which should have exact same charges.

Also, in many cases when the net charges of your modified residues are
not zero, you may want to cap the residues first. Good luck, Frank

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