[gmx-users] gmx does not recognize HIE as protein

[Tsjerk Wassenaar]

Hi Rebeca,

In the GMX data directory ($GMXDATA) there's a file aminoacids.dat
listing what should be recognized as amino acids. Either edit the file
and add HIE (also incrementing the counter at the top line) or make a
local copy of the file in the directory where you need it and edit
that.

Cheers,

Tsjerk

On Tue, Aug 12, 2008 at 5:47 PM, Rebeca García Fandiño
<regafan at hotmail.com> wrote:
> Hello,
> I am trying to simulate a protein that has 2 chains (in a membrane, but the
> problem is in the protein). One of the chains of the protein has 416
> residues and the other 421. I want to simulate it using the amber force
> field, so I have prepared the topology for each one of them and then
> converted them with amb2gmx.pl.
>
> When I do grompp of the complete system I can see that it is only
> considering 821 residues of the protein, and they should be 837!!:
>
> Opening library file
> /gpfs/projects/ub51/ub51077/GROMACS-4.0-DEV/share/gromacs/top/aminoacids.dat
> There are: 157455      OTHER residues
> There are:   821    PROTEIN residues
> There are:     0        DNA residues
>
> The problem is that the program considers residues HIE out of the protein
> (histidines):
>
>   0 System              : 716705 atoms
>   1 Protein             : 12658 atoms
>   2 Protein-H           :  6344 atoms
>   3 C-alpha             :   821 atoms
>   4 Backbone            :  2463 atoms
>   5 MainChain           :  3286 atoms
>   6 MainChain+Cb        :  4038 atoms
>   7 MainChain+H         :  4072 atoms
>   8 SideChain           :  8586 atoms
>   9 SideChain-H         :  3058 atoms
>  10 Prot-Masses         : 12658 atoms
>  11 Non-Protein         : 704047 atoms
>  12 HIE                 :   272 atoms
>  13 dop                 : 238464 atoms
>  14 SOL                 : 464400 atoms
>  15 Na                  :   467 atoms
>  16 Cl                  :   444 atoms
>  17 Other               : 704047 atoms
>
>
> I have tried to use both chains together and repeating the same, but the
> result is the same.
>
> What could I do? Anybody knows why there is a problem with HIE?
>
> Thank you very much in advance,
>
> Rebeca Garcia Fandiño
> Parc Cientific de Barcelona
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623