[gmx-users] add heavy atoms

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 8 08:31:00 CET 2010

Carla Jamous wrote:
> Hello everyone,
> I need a precision, concerning gromacs. In my pdb file, some heavy atoms 
> are missing but I need them for my simulation. So my question is: is 
> there an application in gromacs, that can add automatically these heavy 
> atoms? If not, does anyone have an idea of how can I do this?

It's outside the scope of GROMACS. If it's just an atom or two, then 
building them in with any old molecule builder is probably acceptable. 
If it's a whole loop missing, then some more high-tech might be in 
order. Google MODELLER and links on their webpage. There are certainly 
web-servers out there that will be able to do things for you, but caveat 


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