AMBER Archive (2008)

Subject: Re: AMBER: ff99 and ff03 forcefield parameters

From: Peter Kiss (kisspeter1004_at_gmail.com)
Date: Fri May 23 2008 - 13:42:48 CDT

Dear Vald,
Thank you for the answers and suggestions!!
I will try it.
Thanks!
Peter

2008/5/23 Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>:

> Dear Peter,
>
> I am not an expert in parameter development but I would develop the
> parameters for my residue (I assume you're trying to parameterize a
> non-standard amino acid) strictly following the procedure described for each
> force field version.
> First, I would use Cornell et all ff94 procedure to develop all parameters
> for my residue (including charges). Then, I would refit torsional parameters
> and recalculate charges following Duan et al for compatibility with ff03 or
> follow the procedure described in the ff99SB paper to get parameters
> compatible with ff99SB (for the latter charges do not need recalculation).
>
> I guess a discussion about the accuracy of different parameter development
> procedures would be too long for an email. And anyhow, for such a discussion
> others would be more qualified than me.
>
> vlad
>
>
>
> Peter Kiss wrote:
>
> Dear Vlad,
> Thank you for your response, I'm really very grateful for it.
> A know that the ff99SB force field is a reparametrization of the original
> ff99, and a read the paper. In this forcefield the babckbone dihedrals were
> refitted again at LMP2/cc-pVTZ(-f)//HF/6-31G* theory of level. And the
> charges were the same as in ff94 (HF/6-31g*//HF/6-31G*).And the side chain
> torsional parameters came from the previous ff94 forcefield (where the enrgy
> profiles cam from MP2/6-31G* level)?.
> As far as i know, in ff03 the backbone parameters were derived at
> MP2/cc-pVTZ//HF/6-31G**, and the charges at B3LYP/cc-pVTZ//HF/6-31G**.
> These are clear for me.
> In my case the missing torsional parameter are located in the side chain.
> Therefore which level of theory should I use?
> For a representative fragment I have to carry out HF/6-31G* optimization,
> relax scan, and the energy from MP2/6-31G* calculation (as in ff94). After
> that I have to calculate the resp charges for this small fragment at the
> HF/6-31G*//HF/6-31G* theory (becuase the Etor=Eqm-Emm(non-bonded). And i
> will obtain the appripriate parameters for the missing torsion. It is clear.
> But after i obtained the parameters, should i calculate the
> B3LYP/cc-pVTZ//HF/6-31G** charges for th whole molecule? But with other
> charges the torsional parameters are also differnet. Or not?
> Or I don't understand the parameter development?
> Thank you for your response again, but your help will be very hepful.
> Thanks,
> Peter
>
>
>
> 2008/5/23 Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>:
>
>> Maybe you want to take a look at the force field ff99SB instead of ff03 if
>> you want to avoid any potential problems with compatibility between
>> different charge sets and partially avoid the well known problems of ff99
>> itself.
>>
>> vlad
>>
>>
>> Vlad Cojocaru wrote:
>>
>> Dear Peter,
>>
>> Please take a look at the Duan et al. paper and see how exactly ff2003 was
>> developed. You are right, only the main-chain parameters were refitted, the
>> other torsions were kept from previous amber ff. The ff03 paper claims
>> backward compatibility between ff03 charges and the Cornell et al charge
>> set. If you look at previous mail threads on this list you'll find lots of
>> discussion about using ff2003.
>>
>> The QM methods to derive amber ff parameters are described in the AMBER
>> manual as well as in the references therein.
>>
>> GAFF is a generalized amber ff used for small molecules ..
>>
>> Testing of ff parameters is generally described in the papers that
>> published those parameters. That is always a good starting point for ideas
>> for further tests.
>>
>> Vlad
>>
>>
>>
>> Peter Kiss wrote:
>>
>> Dear Amber Developers and Users,
>> Several days ago a posted a mail on the mailing list, but obtained no
>> answers. Sorry for the new mail, but I'm still confused.
>> If I have a modified amino acid with missing torsional parameter, and i
>> would like to use it with ff03 forcefield, which QM calculations should is
>> use?
>> As far as I know, in the ff03 forcefield only the backbone dihedral were
>> refitted, but the charge scheme is b3lyp/cc-pvtz//hf-631g**. Am I correct?
>> But the dihedral parameters of the sidechains are the same as in the ff99
>> forcefield., where HF/6-31G*//HF/6-31G* charges were applied.
>> My questions are s follows:
>> Why were the side chain torsional parameters not refitted in the ff03
>> forcefield, with another charge model?
>> Which ab initio calculations should I use for torsional paremeter
>> development, and for the charges calculations?
>> Or, alternatively, may I use the parameters from the GAFF forcefield? If
>> yes, minimization, small molecular dynamics calculations, dipole
>> moment/vibrational frequency comparison are enough parameters in order to
>> confirm the goodness of parameters?
>> Thank you for your help in advance!!!!
>> Peter
>>
>>
>> --
>> ----------------------------------------------------------------------------
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuterhttp://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
>>
>>
>> --
>> ----------------------------------------------------------------------------
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuterhttp://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
>>
>>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuterhttp://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
>

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