[AMBER] simulating Modified residue of Cysteine attached to mercury

From: Manish Paul <p.manish88.gmail.com>
Date: Wed, 24 Jul 2013 08:18:21 +0530


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 coordinate
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.

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Received on Tue Jul 23 2013 - 20:00:02 PDT
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