On 26/01/2011 11:10 PM, mohsen ramezanpour wrote:
Dear Justin
I don't want to rely on PRODRG server as others.
I want to do my work as accurate as possible.
Absolutely I read your papar and I know PRODRG present bad results for
estimating free energies.
I want to parametrize my drugs by GROMOS43A1 parameters as you said.
I know completely how to do it.Thanks for your and other user's guidances.
Actually I couldn't find any experimentally data to try to obtain it's
result.Then i have to
do what you said.(re-evaluating force field choice and .....)
Sounds wise.
Can you please say me more about this method?
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!
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.)
Mark
Did you have something like this in your papers?
Thanks in advance for your reply
On Wed, Jan 26, 2011 at 3:14 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
mohsen ramezanpour wrote:
Dear All and specially Dear Dr.Justin
I generated parameters for a typical ligand.
now I want to validate it.
How can I do it?
Please let me know references for doing this.
Of course I have read the article by
Dr.Justin(Alzeimer),Unfortunately I couldn't understand it
completely and very good.
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.
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.
I certainly cannot help you better if you simply say you don't
understand something. What isn't clear?
Is there any other article who has done validation after
parametrization?
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.
-Justin
Thanks in advance for your guidance.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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