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
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