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

Anna Marabotti anna.marabotti at isa.cnr.it
Thu Mar 31 17:43:38 CEST 2011

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 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? 
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
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)
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