Dear Khaled,
recently, I derived Amber parameters (parm99SB, parm14SB) for isopeptide
bonds, i.e. Asn/Asp, Gln/Glu, and Lys residues with a third peptide bond
valency at the side chain. The atomic charges were derived according to
the RESP formalism using the R.E.D. functionality (two conformations).
These modified residues allow peptide bonds via side chains (isopeptide
bonds), but also bonds from sidechain to the terminus of a protein chain
(alpha-omega peptide bonds), like in ubiquitin coupled complexes.
If you are interested, contact me for details. (Unfortunately, things
have not been published, yet.)
Regards,
Anselm
Am 10.02.2016 13:52, schrieb Carlos Simmerling:
> the answer to this depends strongly on your goals and what you plan to do.
> If you want to compare the linear and cyclized peptides, and you use a
> highly optimized protein force field for one and GAFF for the other, it
> will be very difficult to know if the differences are because you used
> different force fields or because of the covalent structure. Isolation of
> variables is crucial here.
>
> You don't need parameters for the entire peptide, just for the modified Asp
> and modified Lys. Then you could use the bond command in leap to create the
> covalent link. You probably need to develop new partial charges, assign
> appropriate atom types (the existing ones for Asp and Lys will not be
> correct), and then develop new dihedral parameters for these atom types if
> any are missing. What approximations you make during these steps depends on
> your project goals.
>
> On Wed, Feb 10, 2016 at 7:12 AM, Mohammed Khaled Tumbi <
> khaledtumbi.gmail.com> wrote:
>
>> Dear Dr. Simmerling:
>> I had a thought of using antechamber to calculate charges.
>> But not sure about validity of GAFF forcefield for a peptide molecule which
>> is 13 amino acid length.
>> Any suggestions how to proceed?/.
>> Regards.
>>
>>
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Received on Wed Feb 10 2016 - 07:00:03 PST
