[gmx-users] add heavy atoms

Carla Jamous carlajamous at gmail.com
Fri Jan 8 08:46:44 CET 2010

Thank you Mark
One last question: is there a certain molecule builder (open-source) you
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.


On Fri, Jan 8, 2010 at 8:31 AM, Mark Abraham <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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