I was thinking that's not such a problem switching tha OPLS-AA, since most
of the atoms in my system are from water, that will remain being spc.
--------------------------------------------------
From: "Lucio Ricardo Montero Valenzuela" <lucio...@ibt.unam.mx>
Sent: Wednesday, April 01, 2009 12:59 AM
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace
PRODRGassigned ones
I wanted the OPLS-UA because my system is large (3 proteins with 2 organic
molecules, in water), and, if the G43a1 forcefield gives me a MD speed of
70
ps/day, an all atom model will result much slower. So what else can I do
to
speed up my MD, to get results in 1-3 months?.
Mensaje citado por David van der Spoel <sp...@xray.bmc.uu.se>:
Lucio Ricardo Montero Valenzuela wrote:
> So it 's better to switch to the OPLS forcefield if I want to compute
> the
> charges?.
> How can I implement the OPLS-UA if my gromacs (version 3.3) only
> includes
the
> OPLS-AA?
We don't support United atom OPLS because Jorgensen himself does not use
it anymore. That if something should indicate for you that the united
atom force field has been superseded by the all-atom. Jorgensen himself
uses OPLS-AA with TIP4P, so this is probably the best recommendation.
Most important, if you chose to use another combination, you basically
have to prove that this "works" as well (whatever that means...)
> Mensaje citado por "Justin A. Lemkul" <jalem...@vt.edu>:
>
>>
>> Lucio Montero wrote:
>>> How about MOPAC to calculate the charges for 3-methyladenine (this
>>> molecule has a charge +1) for using the G43a1 force field?.
>>>
>>>
>> That may not be a bad place to start, but any parameters applied to a
Gromos
>> molecule have to reproduce condensed phase thermodynamic observables.
>> Empirical
>> fitting of the initial parameters may be required. Refer to the
>> primary
>> literature. The reference for the 53a5 and 53a6 parameter sets are
published
>> in
>> JCC, which may provide you with some useful information.
>>
>> -Justin
>>
>>> --------------------------------------------------
>>> From: "Ran Friedman, Biochemisches Inst." <r.fried...@bioc.uzh.ch>
>>> Sent: Friday, March 27, 2009 2:35 PM
>>> To: <bije...@yahoo.com.br>; "Discussion list for GROMACS users"
>>> <gmx-users@gromacs.org>
>>> Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace
>>> PRODRGassignedones
>>>
>>>> Dear Josmar,
>>>>
>>>> You haven't written which force field you plan to use. For OPLS and
>>>> AMBER QM-based optimisation should be fine. In Gromos, the FF was
>>>> developed with the aim of reproducing experimental results and I'm
>>>> not
>>>> sure if you can find a better solution than examining other residues
>>>> with the same chemical moieties or use the same approach as reported
>>>> in the relevant manuscripts. Some software packages can also be
>>>> used -
>>>> these are mostly proprietary and not so easy to use.
>>>>
>>>> Once you derive the parameters, it's a good idea to make some test
>>>> runs of the ligands and see if they behave as expected before you
>>>> actually run a simulation with the protein. For example, if a
>>>> conjugate ring system isn't planar something may be wrong in the
setting.
>>>>
>>>> There's no easy solution - this is why it's considered an advanced
>>>> topic. It is, however, very important. I've encountered a ligand
>>>> that
>>>> leaves its binding site during a simulation due to wrong parameters
>>>> (in this case, the protonation of a protein side chain - FEBS 581,
>>>> Pages 4120-4124, 2007).
>>>>
>>>> Hope that helped,
>>>> Ran
>>>>
>>>> On Fri, 27 Mar 2009 12:22:01 -0700 (PDT)
>>>> "Josmar R. da Rocha" <bije...@yahoo.com.br> wrote:
>>>>> Dear users,
>>>>>
>>>>> I have been reading some posts about using externally computed
>>>>> charges to replace Prodrg charges at ligand topology files. Many
>>>>> users commented on the low trustability given to Prodrg charges
>>>>> (e.g
>>>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ;
>>>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ).
>>>>> Dr. Verli pointed out the use of semi-empirical methods such as RM1
>>>>> in cases not involving simulations with sulphate or phosphate
>>>>> groups
>>>>> (what is not my case) and the use of QM methods with the 6-31G**
>>>>> basis set, for example, to obtain robust charges
>>>>> (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html).
>>>>> On
>>>>> the other hand Dr. Mobley defined as a "a bad idea to compute
>>>>> charges
>>>>> for an all-atom case using QM and then try to convert these to a
>>>>> united atom force field". Other users advice that the best charges
>>>>> are that compatible with the force field parametrization
>>>>> (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ;
>>>>> http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html),
>>>>> usually pointing to
>>>>> http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman
>>>>> suggested that "to calculate the electrostatic potential over the
>>>>> whole molecule, and fit the atomic charges so that they reproduce
>>>>> this potential" in order to make it less sensitive to small changes
>>>>> in the geometry of the molecule may give good results
>>>>> (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html).
>>>>> Dr. Lemkul stressed the need for charges refinement to reproduce
>>>>> experimentally-observed behavior while trying to use QM charges
>>>>> with
>>>>> Gromos ff. since "Parameterization under Gromos usually involves
>>>>> empirical derivation of physical parameters, and free energy
>>>>> calculations using thermodynamic integration". Few examples of
>>>>> protein-ligand studies using Gromacs and Gromos96 ff that I have
>>>>> access (from literature) seem to treat it as "take it for granted"
>>>>> issue (any reference with a more detailed description would be
>>>>> welcome :-)). Despite reading on this topic I could not compile all
>>>>> the information in a clear and objective way (may be because I'm in
>>>>> the wrong track). Let ask you some question that I find would help
>>>>> me
>>>>> to make my ideas more clear:
>>>>>
>>>>>
>>>>> 1-am I overestimating the importance of ligand charges in such a
>>>>> simple study of protein-small molecule (containg charged Phosphate
>>>>> groups) complex? or
>>>>>
>>>>> 1.1-The only way to test for this is doing many different
>>>>> simulation
>>>>> on the same system using different type of computed charges to see
>>>>> what happen?
>>>>>
>>>>> 2-How could I try to choose a method to obtain reasonable charges
>>>>> based on the reproduction of experimentally-observed behavior if I
>>>>> do
>>>>> not have experimental data for my system?
>>>>>
>>>>> 3-I also would like to know from users dealing with protein-ligand
>>>>> interactions studies what do you consider a good approach to
>>>>> address
>>>>> this problem?
>>>>>
>>>>> Based on what I read I'd have a tendency to use HF/6-31G** ESP
>>>>> derived charges (with necessary changes as to make it united-atom
>>>>> charges and scaling that to a integer number for each group).
>>>>> Please,
>>>>> let me know if that strategy would be as good as a disaster! Thank
>>>>> you very much for the attention.
>>>>>
>>>>>
>>>>> Josmar Rocha
>>>>>
>>>>>
>>>>>
>>>>> Veja quais são os assuntos do momento no Yahoo! +Buscados
>>>>> http://br.maisbuscados.yahoo.com
>>>>
>>>>
>>>> _______________________________________________
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
> Lucio Ricardo Montero Valenzuela
> Instituto de Biotecnologia, UNAM
> Departamento de Biologia Molecular de Plantas
> Av. Universidad 2001, Col. Chamilpa
> Cuernavaca 62210
> Mexico
>
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico
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