I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein.<div>
shahid nayeem<br><br><div class="gmail_quote">On Thu, Aug 11, 2011 at 3:15 PM, 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 11/08/2011 7:24 PM, shahid nayeem wrote:
<blockquote type="cite">Hi Justin
<div>I prepared a box of SOL and arginine Hydrochloride. But when
I solvate my protein with this box now the positively charged
arginine is as solvent and this causes problem in grompp. It
gives error like "No such Molecule types ARG" etc. Solvating
arginine with water and preparing a box was without error. which
forcefield in gromacs has inbuilt .itp file for free amino acid
which I can include in my .top file.</div>
</blockquote>
<br></div>
See <a href="http://www.gromacs.org/Documentation/How-tos/Multiple_Chains" target="_blank">http://www.gromacs.org/Documentation/How-tos/Multiple_Chains</a>.
Pre-position the non-water molecules, use pdb2gmx, solvate.<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote type="cite">
<div>Shahid Nayeem<br>
<br>
<div class="gmail_quote">On Fri, Jul 29, 2011 at 5:02 PM, Justin
A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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">
<div><br>
<br>
shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All I am trying to find the topology and
parameterof free Arginine Hydrchloride molecule in
gromacs force-field format. Developing it in Pro-Drg
will not serve as I will need some other
parametrization tool to check it charges. If someone can
help, I will be grateful.<br>
</blockquote>
<br>
</div>
Isn't this just a protonated arginine (normal state for
neutral pH) with a chloride counterion? There's nothing
special about it, just run a coordinate file through pdb2gmx
with the force field of your choice.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<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> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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