[gmx-users] Is TRO defined correctly in the ffG43a1p forcefield file?

[Justin A. Lemkul]

Kirill Bessonov wrote:
> Dear all,
> 
> I am trying to run simulation with phosphorylated Threonine (TRO) and I 
> found lot's of info about this issue reading previous posts which 
> explained on how to patch the force-field files and define this modified 
> amino acid. After looking at the community forcefield offered 
> here http://www.gromacs.org/Downloads/User_contributions/Force_fields
> 
> After exploring those files what calls my attention is that in the *.hdb 
> file that describes which atoms are protonated is seems to have an issue 
> that I wanted to double-check with the rest of the members. It seems to 
> me that  the CH3 group is not protonated in the phosphotyrosine (TRO) as 
> shown below
> 
> Extracted from *.hdp file
> THR     2       
> 1 1 H N -C CA
> 1 2 HG1 OG1 CB CA
> 
> TPO     1
> 1       1       H       N       -C      CA
> ...but where is the 2nd line???
> 
> Why THR has 2 lines why the TRO having the PO3 group has only one line? 
> Can somebody explain this?
> 

There is only one polar H in TPO.  Read the .rtp entry for TPO - it states that 
it is the -2 form of the phosphorylated residue.  The HG1 atom connected to OG1 
is removed with the formation of a phosphoester in the modified sidechain.  TPOH 
is the -1 form of the phosphate and thus there is a proton on the phosphate group.

-Justin

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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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