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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Received on Wed Jun 26 2013 - 08:30:02 PDT
