Thank you Mark<br>One last question: is there a certain molecule builder (open-source) you recommand.?<br>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.<br>
<br>Carls<br><br><div class="gmail_quote">On Fri, Jan 8, 2010 at 8:31 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello everyone,<br>
<br>
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?<br>
</blockquote>
<br></div>
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.<br>
<br>
Mark<br><font color="#888888">
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