AMBER Archive (2007)

Subject: AMBER: Antechamber esp calculation

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Mon Jan 22 2007 - 22:44:42 CST

Dear amber community,

    I have a doubt about the parametrization of some modified nucleic acid residues.
We are trying to generate the parameters by doing Gaussian calculation. The residues have a charge of -1. The molecule after optimzation at HF-6G* is distorted about the phosphate group. The espgen is not producing any output files from the gaussian output files. There are not any error messages also. The pdb file of the residue amd the gaussian output files are attached. Please advice me what to do.

I have one more question. Is it raesonable to do a singlepoint calculation to get the esp, if it is an experimental structure?

Thanking you

Mathew

                                 
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