Dear Dr Mark<br>Thanks for your guidances.<br>I am sorry for my last question.My english is not very good,I hope I could say what was in my mind not what you read :-)<br>by the way,Thanks for your attention and your reply.<br>
<br><div class="gmail_quote">On Wed, Jan 26, 2011 at 3:55 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 26/01/2011 11:10 PM, mohsen ramezanpour wrote:
<blockquote type="cite">Dear Justin<br>
I don't want to rely on PRODRG server as others.<br>
I want to do my work as accurate as possible.<br>
Absolutely I read your papar and I know PRODRG present bad results
for estimating free energies.<br>
I want to parametrize my drugs by GROMOS43A1 parameters as you
said.<br>
I know completely how to do it.Thanks for your and other user's
guidances.<br>
Actually I couldn't find any experimentally data to try to obtain
it's result.Then i have to <br>
do what you said.(re-evaluating force field choice and .....)<br>
</blockquote>
<br></div>
Sounds wise.<div class="im"><br>
<br>
<blockquote type="cite">
Can you please say me more about this method?<br>
</blockquote>
<br></div>
It sounds to me like he's said plenty of useful things on the topic
:-) A question with a precise focus is much more likely to attract
somebody's interest. Otherwise, it can sound too much like you're
asking for your work to be done for you!<br>
<br>
Back on point, if you can't determine a basis for the kind of
empiricism GROMOS forcefields require, then you may want to choose
one of the other force fields with a more automated method. That
doesn't remove the need to validate, or the conundrum if validation
fails, however. It's very easy to do a worthless simulation. Many of
them are. Many more of them become so because they don't describe
enough detail that they could be reproduced. For example, lots of
people say just "I used PME with x cutoff" in the same way they did
in the 1990s when they used a plain cutoff. I've read three such in
the last week. However, that statement is almost useless as an
indicator of quality in the electrostatic model. (Oops, I've
digressed. Oh well.)<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">Did you have something like this in your papers?<br>
Thanks in advance for your reply <br>
<br>
<div class="gmail_quote">On Wed, Jan 26, 2011 at 3:14 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All and specially Dear Dr.Justin<br>
I generated parameters for a typical ligand.<br>
now I want to validate it.<br>
How can I do it?<br>
Please let me know references for doing this.<br>
Of course I have read the article by
Dr.Justin(Alzeimer),Unfortunately I couldn't understand it
completely and very good.<br>
</blockquote>
<br>
</div>
I will assume that you're still using one of the Gromos force
fields for your work. Gromos parameterization relies on
reproduction of condensed-phase behavior, in theory, the
partitioning of the species of interest between hydrophobic
and aqueous media. Ideally, you would calculate deltaG of
hydration in different media, but such information is not
always readily available. That's why I turned to an alternate
approach in the paper you mention, but one that holds in the
same spirit of the force field and for which I had
experimental evidence with which to compare.<br>
<br>
If you don't have any suitable experimental data regarding
your ligand, you should re-evaluate your force field choice
and consider whether or not parameterizing a bunch of unknown
compounds is a viable approach.<br>
<br>
I certainly cannot help you better if you simply say you don't
understand something. What isn't clear?
<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Is there any other article who has done validation after
parametrization?<br>
</blockquote>
<br>
</div>
Some, but (unfortunately) not many. Numerous authors seem to
blindly rely on PRODRG, which was the motivation behind our
most recent work (in JCIM, which I believe you said you've
read). See the references therein for a few examples of
attempts that have been made to derive and validate proper
parameters. More rigorous standards are really necessary to
avoid potential inaccuracies in these types of simulations.<br>
<br>
-Justin
<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks in advance for your guidance.<br>
<br>
</blockquote>
<br>
</div>
-- <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>
========================================<br>
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