Re: [AMBER] simulating Modified residue of Cysteine attached to mercury

From: FyD <>
Date: Wed, 24 Jul 2013 09:58:12 +0200

Dear Manish,

See R.E.D. Server Development at
   (vs R.E.D. Server at

All should be re-opened tonight...

If you decide to use R.E.D. Server Development (compatible with all
the elements of the periodic table) - as you underlined in your email
- pay attention to the atom names you use in the PDB input file; for
. HG/Hg/HG1 should be recognized as a mercury atom (& not as an hydrogen atom)
. CA as ... Calcium and not as a alpha carbon
. same problem for NA, CO, CL (Fe vs F) etc...
(R.E.D. Python provides a way to differentiate HG as a mercury or a
hydrogen atom and more generally all these ambiguities).

We can also post-process the data you will obtained using R.E.D. IV by
using R.E.D. Perl where the atom types, and frcmod files will be
automatically generated for all the elements of the periodic tables...

regards, Francois

> 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.

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Received on Wed Jul 24 2013 - 01:00:05 PDT
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