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 - 03:00:02 PDT
