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

[Rebeca García Fandiño]

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.datThere are: 157455      OTHER residuesThere are:   821    PROTEIN residuesThere 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
 
 
_________________________________________________________________
¿Preparándote para el verano? En Windows Live Search encontrarás las mejores dietas para conseguir tu peso ideal
http://search.live.com/results.aspx?q=dieta&form=MKTPG
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080812/01562f15/attachment.html>