Dear Dr Mark Thanks for your guidances. 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 :-) by the way,Thanks for your attention and your reply.
On Wed, Jan 26, 2011 at 3:55 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > 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> 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 | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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