---------- Forwarded message ----------
From: madhumita das <madhumita.bioinfo.gmail.com>
Date: Sun, Aug 7, 2011 at 7:41 AM
Subject: simulating Modified residue of Cysteine attached to mercury
To: amber.ambermd.org
Sir,
I want to generate prmtop and prmcrd files by using the xleap
module of Amber for a modified cysteine residue having mercury atom attached
to its sulphur(CysSHg+),how to add mercury in Amber? what are the initial
files (including force field files) it needs to generate topology and co
ordinate files? What should be the symbol of mercury in the pdb file?
because it assumes Hg as H whenever i run antechamber to generate prep and
mol2 files, I am confused how and where to add forcefield parameters in
amber to get parameter and topology file,can I proceed further to do MD
simulation in GROMACS by converting topology and coordinate file in .gro
format,what are the files to be modified in GROMACS to complete my
simulation? Please Help,waiting eagerly.
Thanks in advance.
Madhumita Das
Bioinformatics Trainee
University of Kalyani,India
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Received on Tue Aug 16 2011 - 04:30:05 PDT
