[Fwd: [gmx-users] preferred/best force fields]

iulek at interponta.com.br iulek at interponta.com.br
Tue Aug 18 18:13:16 CEST 2009

Dear Mark,

    Thanks for your input. Maybe it does not fit exactly what I would  
like (should there be what I would like), but it brings me worthy  
information to clear my vision on how I might carry this on.


> iulek at interponta.com.br wrote:
>> Hi,
>>     I see there are many interesting topics going on, maybe due to  
>> this I did not receive any answer/suggestion/comment to my question  
>> or maybe it is rather naive. Anyway, it would like to listen to the  
>> experts if there are no other suggestions to add to what I did below.
>>     Thanks,
>> J.
>> -------- Original Message --------
>> Subject:     [gmx-users] preferred/best force fields
>> Date:     Fri, 14 Aug 2009 12:35:18 -0300
>> From:     iulek at interponta.com.br
>> Reply-To:     Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To:     gmx-users at gromacs.org
>> Dear All,
>>     I am new to molecular dynamics, had some tutorials and could run
>> some initial tests successfully in that they finished without errors
>> (now to analyze if results make sense).
>>     Now my challenge is to make a molecular dynamics of a homohexamer
>> which binds to a ssDNS and a co-factor, and that loses some of its
>> binding capacities when a mutation is present. I could build an
>> (non-hydrogen) homology model for the system, but I am still facing
>> some problem on conventions for atom names. I could not overcome
>> everything still, though.
>>     But in this post I would like to discuss about the best force
>> fields to use in the main problems I should face: a) a protein monomer
>> in water; b) a protein oligomer in water; c) a protein bound to an
>> inhibitor (small organic molecule) in water; d) a protein homohexamer
>> bound to DNA and co-factor in water.
>>     I spent the last days gathering some information through the web
>> and the gromacs manual. I could learn a lot, but I feel I still miss
>> some organization of my understanding. It seems to me that specially
>> for case "d" (the very one of the moment) an amber force field port
>> (which best, 99SB?) to gromacs should be the preferred one, right?
>> Anyway, I would like to make the question wider and ask if someone
>> might point me to an article/links/whatever, for the to mature this
>> overview, id est, to a compilation of the preferred (or best) force
>> field for some typical biochemical MD simulations.
> Answering that series of questions might take a new PhD student a  
> month or more of reading, and there still won't be much in the way  
> of definitive answers! You should start by finding some suitable  
> recent review articles, and tracing the articles to which it refers.  
> I don't have one to hand, however. Also, you need to find and read  
> some work that someone has done on a similar system and see whether  
> they came up with plausible simulation results. In principle, I  
> understand CHARMM and AMBER forcefields are supposed to be able to  
> deal with such systems, but you will need to do your own legwork  
> there.
> Mark
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