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
--
========================================
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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