AMBER Archive (2007)

Subject: Re: AMBER: Antechamber esp calculation

From: FyD (fyd_at_u-picardie.fr)
Date: Tue Jan 23 2007 - 00:05:46 CST

Quoting mathew k varghese <mathew_kvarghese_at_yahoo.co.in>:

> 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.

Because of the -1 negative charge.

> 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.

Usually the charge values fo a new nucleotide are derived using two
different molecules: dimethylphosphate + the corresponding nucleoside.
See, for instance, the F-57, F-58 and F-59 REDDB projects,
http://www.u-picardie.fr/labo/lbpd/REDDB/, F-60 being more complex.

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

You need indeed to run a single point calculation to get the molecular
electrostatic potential.

regards, Francois

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