[gmx-users] add heavy atoms

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 8 09:29:18 CET 2010

Carla Jamous wrote:
> Thank you Mark
> One last question: is there a certain molecule builder (open-source) you 
> recommand.?

No, the one I use isn't open.

> Because all the molecule builders I found, draw molecules from scratch, 
> but what I need is to add heavy atoms to the pdb structure I already have.

Probably they can all load an existing PDB structure and save a modified 
one. It's very standard function.


> On Fri, Jan 8, 2010 at 8:31 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     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 emptor.
>     Mark
>     -- 
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