HEME A and Re: [gmx-users] modeling unnatural amino acids

Markus O Kaukonen mokaukon at cc.helsinki.fi
Fri May 17 12:20:10 CEST 2002

Dear *,

Similarly than Rich McClellan (See below) I try to make an
*rtp entry for a heme structure that is slightly
different than the existing one (HEME) in ffG43a1.rtp

I proceed defining a new entry for HEA in ffG43a1.rtp (see below),
mainly copying existing HEME entry.
But it seems to me that one should define the two bond parameters
in the [bonds] section for each pair.
There seems to be pre-defined parameters which I'd like to use
(in file ffG43a1bon.itp entries like
 #define gb_26       0.1530  7.1500e+06
 ; C, CHn  -   C, CHn    800

So the question:

1) Is there a way to avoid putting all bond parameters in [bonds]
   section in the ffG43a1.rtp file but letting pdb2gmx choose the ones
   based on atom types of near-by atoms?

   If one has to put the bond parameters by hand to ffG43a1.rtp can
   pdb2gmx then generate [angle] [dihedral] [impropers] and non-bonded
   That would be too big job for me to do manually (system of ~60 atoms).

2) In case one has to give the bond parameters in [bonds] section:
   Is there more documention of the kb and b0 parameters defined in
   ffG43a1bon.itp for the bonds?
   I mean, for example, just to know what parameter to
   take for C-C single or C=C double bond in a hydrocarbon chain.

I guess this is a problem of general interest and it would be nice to have
step-by-step intructions for beginners how to include new building
blocks to the gromacs-database in as computer assisted as possible.
This assuming that one trusts the parameters already existing in the
gromacs database and does no parameter fitting.

Best Wishes, Markus

Rich McClellan wrote:

> Hi,
> I have a peptide composed of unnatural amino acids that I'd like to
> model with GROMACS.  GROMACS (pdb2gmx) is unable to calculate the
> molecular topology of the system and gives an error message stating that
> the residue is not found in the topology database.
> Generating the topology file from hand looks daunting so I was wondering
> if somebody has developed a topology database of "other" amino acids or
> have suggestions on the best way to proceed.
>         thanks in advance,
>         Rich

Erik Lindahl wrote:

Hi Rich,

It's not too difficult to add a new residue to the topology database.
Have a look in the file ff<name>.rtp, where <name> is the force field
you are using.

You can probably copy most parts from a standard amino acid that is
similar to your new one. There are three parts for each residue:

This section maps names found in the pdb file (col 1) to atom types (col
2), charge (col 3) and charge groups (col 4). Try to have neutral charge

Just define the connectivity in the residue. Names prepended with a dash
("-") refer to atoms in the next residue, if present.

Define the improper dihedrals needed to maintain chirality of the

That's it - everything else like angles, normal dihedrals, and the
actual parameters will be generated by pdb2gmx.



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