Quoting mathew k varghese <mathew_kvarghese.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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 24 2007 - 06:07:33 PST
