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.eml-r.villa-bosch.de
> <mailto:Vlad.Cojocaru.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://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 Reuter
>> http://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://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 Reuter
> http://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 Reuter
http://www.eml-r.org
----------------------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun May 25 2008 - 06:07:53 PDT
