[gmx-users] "How to include topologies for non-standard residues occuring within the protein chain"

Leon Salgado vesbes2003 at yahoo.com
Fri Jun 20 02:33:01 CEST 2003

Hi gmx's

Have to say that I searched in the gmx mail list and
also the manual, but I'm still a little bit confused.
My aim with this e-mail is to gather some information
about how to include new residues into a non-standard

PRODRG produced an .itp file, for a formilated residue
that I have built in insightII.  This residue belongs
to the primary structure of my protein. So basically,
I have been searching for the know how to build the
top and gro file for my system, using the pdb2gmx

 From what I read, we can build this new residue inside
the rdp of the ff to be used, not forgetting to change
the hdb entry.

Is there other way (copying and pasting/editing from
the drg itp to the rtp file, I mean)?, since I have
already the .itp file for that residue?

The most coherent mail that I saw about this subject
was from Dr. Paul Barret : [gmx-users] sridhar: How to
include topologies for unusual/phosphorylated residues
occuring within the protein chain; Fri May 16 11:05:01
2003. Just for the forgotten one's:

... here is how I did it for phosphorylated Threonine.

1) open the appropriate .rtp file e.g. ffG43a1.rtp
2) make a copy of the existing entry for the residue
you want to phosphorylate it.

here are the notes I made as I did it...comments
welcome if anyone
doesnt like how I did it!

; TPO which follows is phosphorylated Threonine and
was derived thus:
; 1) take THR entry
; 2) add P, O1P, O2P, O3P atoms
; 3) remove HG1 atom
; 4) assign partial charges to give an overall
molecule -2 charge
;     with this charge localised on the Phosphate
; 5) add bonds for OG1 to P and the OxPs. took bond
tpyes from [ DADE ]
; 6) likewise took angle types from [ DADE ]
; 7) removed final dihedral which contained H1 (had
considered changing
it for
;     P but dont want to limit Phoshphate group too

3) you will need to add the new residue to the file
aminoacids.dat if
you want the residue to be recognised as part of the
protein in
subsequent analysis. Make sure you increment the count
on the top line
of aminoacids.dat. dont put any comments in
aminoacids.dat becuase it
has unpredictable effects on results.
4) update the hydrogen database entry too if you are
expecting pdb2gmx
or protonate to work properly.

I *think* that was it...!
Paul Barrett

A good protocol to follow. But, and if I added some
atoms that didn't belong to any of the atomtypes known
to the ffield?  

Several gmx-users answer to new gmx-users like this:
take a look to Kerrigan's GROMACS Tutorial for
Drug-Enzyme Complex.  Well, that tutorial only applies
to 2 or more non-covalent structures. It's not the

Thought in the possibility of making a new entry (e.g.
 a formyl group) in ff**-n.tdb (my formilated residue
is the N terminal one). Will it be be possible to do

Leon Salgado

P.S. Sorry if I'm messing up the concepts. 

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