From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Sun Jun 30 2013 - 14:02:06 CDT
Hi,
Download the *.mol2 version of nitrite and nitrate molecules from zinc database: zinc.docking.org/
Special attention to protonated state of molecules at pH 7.0 (or other desired pH).
Submit each of them to www.swissparam.ch/
Download toppar and param files in Charmm format (*.zip).
If you want accurate force fields, optimize molecules with B3LYP/6-31G++(d,p) level of theory and replace partial charges at toppar files generated by Swissparam.
Regards,
-------------------------------------
Flavio Augusto Vicente Seixas
Laboratory of Structural Biochemistry
Department of Biochemistry
Universidade Estadual de Maringá, PR, Brazil
http://www.uem.br
________________________________
From: "amin_at_imtech.res.in" <amin_at_imtech.res.in>
To: namd-l_at_ks.uiuc.edu
Sent: Saturday, June 29, 2013 2:51 PM
Subject: namd-l: Topology and parameters for nitrate and nitrite ion
Dear NAMD users,
I want to run a simulation of a protein with bound nitrite and nitrate ions. Can
someone please guide me on how/where to obtain the topology and parameter files
for these ions? Any suggestions will be highly appreciated.
Regards.
Amin.
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