Michael McGovern wrote:
Hi everyone.
I'm working on getting parameters for a protein system that has some
linker residues in it. These linkers are nothing too strange, they just
have some amine groups. I can get bonded parameters from the prodrg
server. I know the charge groups are unreliable. I'm using the 53A6
parameter set, and I read how the charges there were derived. They
specifically did the iteration of parameters manually to give the same
charges for the same functional groups. Does this mean I can take
charges from the same functional groups in the rtp files for amino acids
and use those charges in my linkers? If it is necessary to validate,
should that be done on the linkers as molecules in their acidic,
unlinked form?
Thanks everyone.
Generally, the functional groups in the GROMOS parameter sets are very
transferrable, as their derivation scheme would suggest. I suppose about the
only validation you could do would be to prove that the properties of your
linker molecules (whatever they may be) are reproduced by the application of
these parameters when not joined to your protein. Reproduction of
condensed-phase behavior and thermodynamic properties was the goal of the GROMOS
derivation.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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