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

[Markus O Kaukonen]

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
   parameters?
   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:

[atoms]
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
groups.

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

[impropers]
Define the improper dihedrals needed to maintain chirality of the
molecule.


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

Cheers,

Erik

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