<div dir="ltr">Ok. I did some "dockings" with know conformation of the protein comlex. The experiment was take the crystallographic complex, obtain the coordinates of each protein in the complex, did the docking experiment to re built the complex, then, take the best complex and to refine it with MD simulation. The best result was opls/aa (the rmsd with the crystallographic complex was less of 1 A). But that experiment was a few years ago, maybe the new forcefields are better now (you can try something similar to test it).<br>
<br>Maxi <br><br><div class="gmail_quote">On Thu, Sep 11, 2008 at 1:10 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">
Maximiliano,<br>
<br>
Could you give some more argumentation regarding your choice of<br>
opls-aa? What tests did you use and what were your criteria? Did you<br>
verify against experimental data?<br>
<br>
Paula,<br>
<br>
I wouldn't go for Gromos 43a1 and most certainly not for ffgmx. The<br>
latter is completely obsolete, and the former likely should share that<br>
qualification. It's superseded by their newer force fields, 43a2/45a3<br>
and 53a5/53a6. The last two of these are the result of a new<br>
philosophy behind the parameterization. Check the papers if you want<br>
to know more.<br>
Since you're dealing with ligands of which I'm not sure whether the<br>
(newer) GROMOS force fields can handle them correctly, maybe Alan's<br>
suggestion to try Amber/Gaff is not so bad.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<div><div></div><div class="Wj3C7c"><br>
On Thu, Sep 11, 2008 at 2:55 AM, Maximiliano Figueroa<br>
<<a href="mailto:maxfigue@gmail.com">maxfigue@gmail.com</a>> wrote:<br>
> I was working with protein complex, and after tests some FF, I could obtain<br>
> best results with oplss/aa<br>
><br>
> On Wed, Sep 10, 2008 at 12:07 PM, Alan <<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>> wrote:<br>
>><br>
>> Short answer, try Amber99SB with Gaff.<br>
>><br>
>> Alan<br>
>>><br>
>>> Message: 1<br>
>>> Date: Fri, 5 Sep 2008 15:06:21 +0200<br>
>>> From: " Paula Gonz?lez-Rubio " <<a href="mailto:paula.grg@gmail.com">paula.grg@gmail.com</a>><br>
>>> Subject: [gmx-users] which force field for a protein-protein complex?<br>
>>> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>>> Message-ID:<br>
>>> <<a href="mailto:2408dbb80809050606k52d73eafsd87f6b54987d6713@mail.gmail.com">2408dbb80809050606k52d73eafsd87f6b54987d6713@mail.gmail.com</a>><br>
>>> Content-Type: text/plain; charset="iso-8859-1"<br>
>>><br>
>>> Hello there,<br>
>>><br>
>>> I would like to do a MD of a protein-protein complex (both with their<br>
>>> ligands) so I'm looking for some advise regarding the best force field<br>
>>> for<br>
>>> simulate my system. For more details, it consists on a ADP-ribosylase<br>
>>> (which<br>
>>> ligand is the NAD) and a small G protein (GDP binded), we want to see<br>
>>> what<br>
>>> is the role of a loop in the formation of the complex and on the<br>
>>> ADP-ribosilation of the small G protein.<br>
>>><br>
>>> Does any one have a good idea of an appropiate force field for this kind<br>
>>> of<br>
>>> systems ? Do you think gromos 43A1 or ffgmx could be an option?<br>
>>><br>
>>> Thanks a lot in advance!<br>
>>> Paula<br>
>>><br>
>>><br>
>>> -- !!!!! NEW email !!!!!!<br>
>>><br>
>>> <a href="mailto:paula.grg@univ-paris-diderot.fr">paula.grg@univ-paris-diderot.fr</a><br>
>>><br>
>>><br>
>>> ******* NEW ADDRESS ******<br>
>>> Paula GONZALEZ-RUBIO<br>
>>> PhD Candidate<br>
>>> DSIMB INTS, INSERM UMR-S726<br>
>>> 6 rue Alexandre Cabanel 75015 Paris<br>
>>> Tel : +33(1) 44 49 30 00 Fax : +33(1) 47 34 74 31<br>
>>> 4th Floor. Room 401 Bis<br>
>>> Web Site:<br>
>>> <a href="http://www.dsimb.inserm.fr/" target="_blank">http://www.dsimb.inserm.fr/</a><<a href="https://paris7.jussieu.fr/Redirect/www.dsimb.inserm.fr/" target="_blank">https://paris7.jussieu.fr/Redirect/www.dsimb.inserm.fr/</a>><br>
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>>><br>
>>> --<br>
>><br>
>> --<br>
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
>> Department of Biochemistry, University of Cambridge.<br>
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>> >><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
>><br>
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<br>
<br>
<br>
</div></div>--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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