[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
recommand.?
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.

Carls

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100108/03627b2c/attachment.html>


More information about the gromacs.org_gmx-users mailing list