Hi Sophia,
I did something similar using the parm99SB set and RED to derive
charges. Here is the reference (take a look to the supporting material,
where a better description of computational methods is given):
1H-azepine-4-amino-4-carboxylic Acid: a New alpha,alpha-Disubstituted
Ornitine Analogue Inducer of Helix Conformations in short Ala-Aib
Pentapetides."
S. Pellegrino, A. Contini, F. Clerici, A. Gori, D. Nava, M. L. Gelmi
/Chem. Eur. J./, *2012*, /18/, 8705--8715
Regards
Alessandro
Il 26/06/2013 17:19, Cheng-I Lee ha scritto:
> Dear Karl,
>
> Thanks for your suggestion!
>
> Sophia
>
>
> On Wed, Jun 26, 2013 at 5:41 PM, Karl N. Kirschner <
> kkirsch.scai.fraunhofer.de> wrote:
>
>> Hi Sophia,
>>
>> I now that parm99SB has some parameters for F, but I don't know if they
>> will encompass your molecule. This depends on which hydrogen atom you do
>> the substitution on. According to the comments within the force-field file,
>> the bonded parameters come from "JCC,13,(1992),963"
>> "JCC,7,(1986),230" and "Junmei et al, 1999" (as found in
>> $AMBERHOME/dat/leap/parm/parm99.dat of my amber12 installation). I am not
>> sure how often these parameters have been implemented, so a good literature
>> search starting from these references would be appropriate.
>>
>> If you want to test the existing parameters, or if you need to optimize
>> or develop new one for your residue, you could use Wolf2Pack to do so (I
>> will have to upload some appropriate molecules to its database though).
>> Antechamber is another option that will borrow parameters from the gaff
>> force field. Even then you may have parameters that are set to zero and
>> require attention. The R.E.D. server will enable you to develop partial
>> atomic charges for the modified amino acid residue that is well balanced
>> with the rest of the protein force field.
>>
>> My suggestion as a starting point is to build your peptide and run it
>> through xleap to see if and what missing parameters exist.
>>
>> Cheers,
>> Karl
>>
>>
>> ----- Original Message -----
>> From: "Cheng-I Lee" <biocil.ccu.edu.tw>
>> To: "AMBER Mailing List" <amber.ambermd.org>
>> Sent: Wednesday, June 26, 2013 11:14:43 AM
>> Subject: [AMBER] Force-field for non-native peptide containing fluoride
>>
>> Dear all,
>>
>> I would like to do MD simulation for a non-native peptide containing
>> fluoride (one H is replaced by F). What force-field would you suggest?
>>
>> Thanks for your help!
>> Sophia
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--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
ResearcherID: F-5064-2012
URL: http://www.researcherid.com/rid/F-5064-2012
skype alessandrocontini
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Received on Wed Jun 26 2013 - 09:00:03 PDT
