topology and parameter file for non aromatic nitrogen in ring system.

From: Dhiraj Srivastava (
Date: Thu Aug 17 2006 - 22:15:57 CDT

Hi all
        does anyone have any information about topology and parameter file
for any molecule which has a non aromatic nitrogen in cyclic ring system. i
want to create structure file with deprotonated Proline amino acid (not
residue) but by default psfgen generate its zwiterionic form. so i want to
create topology file for deprotonated form of Proline amino acid by
myself. Histidine has a nitrogen atom in 5 member ring system but that
nitrogen is aromatic in all protonated form of His. ring nitrogen
in nucleotide bases are also aromatic or near the carbonyl carbon. so the
charge on these nitrogen atoms will be different than that of deprotonated
Proline amino acid. i have searched the topology files available on the
website and
found that charge status of secondary and tertiary amine are different.

thank you in advance for your help

Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153

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