[gmx-users] adding a new residue in the ff

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 31 19:13:22 CEST 2011

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.


> 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: amarabotti at isa.cnr.it <mailto:amarabotti at 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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