Actually, I am planning to use AMBER forcefield for both phosphotyrosine and for the system too. The parameters are reliable as they have been published (<a href="http://www.springerlink.com/content/u527364w03568353/fulltext.pdf">http://www.springerlink.com/content/u527364w03568353/fulltext.pdf</a>) . But I want to know how to add them to the force field. I have checked the following link :- <a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>, but I want to do it in a rather shorter way. Like what has been done in the protein ligand tutorial. But will that be ok to do. As in my case also I too have a docked complex . <br>
<br><div class="gmail_quote">On Wed, Jun 8, 2011 at 10:26 PM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" link="blue" vlink="purple">
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<div style="border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt">
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">What forcefield is that for? Sounds like it is more than likely one of the AMBER ones.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">What forcefield are you using for the rest of your system that you are simulating?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Are they the same? They should be.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">If not, are they compatible? A minor number of them are compatible to some degree, such as with a version change for a given forcefield. However, vast majority
are not and combining those that aren’t compatible them will make a nice random number generator that you can spend lots of time using and not get anything out that is publishable.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">See
<a href="http://www.gromacs.org/Documentation/Terminology/Force_Fields#Usage" target="_blank">http://www.gromacs.org/Documentation/Terminology/Force_Fields#Usage</a> and the first point at
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a>
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;color:#1F497D">
</span><span style="font-size:11.0pt;color:#1F497D"><u></u><u></u></span></p>
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