For example if I have a polystyrene polymer chains and monomers of user defined solvent . I need to construct the .itp file by hand . <div><br></div><div>Thanks for the reply</div><div>Kirtana<br><br><div class="gmail_quote">
On Tue, Feb 28, 2012 at 5:31 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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kirtana S wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Users,<br>
<br>
In the gromacs manual on means to convert the pdb file to gromacs topology file I need to use pdb2gmx. Here I have to specify the force field .How to work with organic residues which do not exists . Since I had used general amber force field, and could not find this in the /share/top/ directory . Do I need to manually construct the .itp file for each residues. What will be the easiest way to construct<br>
a solvated box with user defined residues in gromacs.<br>
<br>
</blockquote>
<br></div></div>
If the residue of interest will be a component of a polymeric molecule like a protein, refer to <a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/Adding_<u></u>a_Residue_to_a_Force_Field</a>. If the molecule is a standalone species like a ligand, solvent, etc then all you have to do is #include an .itp file in the system topology.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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