Re: Topology and parameters for nitrate and nitrite ion

From: flavio seixas (
Date: Sun Jun 30 2013 - 14:02:06 CDT

Hi, Download the *.mol2 version of nitrite and nitrate molecules from zinc database: Special attention to protonated state of molecules at pH 7.0 (or other desired pH). Submit each of them to 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 ________________________________ From: "" <> To: 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. ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202

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