Anna Marabotti wrote:
Hi folks,
I have a problem with a "strange" residue into a PDB file. It is a
cysteinesulfonic acid, in which the -SH moiety of the Cys residue is
replaced by -SO3. This modified residue is essential for the activity of
this protein, therefore I must keep it into the protein. So, I'm trying
to add this new residue to the force field (I'm planning to use the
43a1ff already modified for lipids in the past). Since I have Gromacs
4.5.3 I copied the ff directory on my local dir, then I attempted to
modify the aminoacids.rtp file and other files following instructions in
the section "Adding a residue to a force field". In order to have some
hints on OCS topology, I used PRODRG, at least to have some indication
on atom, bonds and angle types, but in the .itp file obtained from
It would probably be easier, faster, and more accurate to just use most of the
parameters for Cys rather than try to have PRODRG re-create a (potentially
flawed) model of your compound. The only new parameters are related to SO3, so
the rest should be identical to the Cys residue.
PRODRG there are several data for which I don't find the corresponding
element in the ffbonded.itp file. For example, I don't see any
equivalent for the CB - SG - OD1 angle. Probably I should add them to
the ffbonded.itp file, but I'm unsure how to do it. Is there an order
to follow, or can I simply add a new element at the end of the [ angle ]
section? Can anyone give me some hint to do it correctly, and more
generally to manage correctly the whole problem?
This is where parameterization becomes a chore - when there's nothing analogous
to what you're doing. Proper Gromos96 parameterization methodology would
dictate that you generate an analogous compound (i.e., methyl sulfonic acid) and
adjust its parameters such that it reproduces various condensed-phase
thermodynamic and physical properties (DeltaG of solvation, liquid density, heat
of vaporization). Proper derivation is quite time-consuming. Perhaps someone
has already done this work and it is published. If you're unlucky, you've got
to do it all yourself.
-Justin
Thanks a lot
Anna Marabotti
__________________________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabo...@isa.cnr.it <mailto:amarabo...@isa.cnr.it>
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)
--
========================================
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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