[gmx-users] add heavy atoms
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
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.
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