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Hello,<BR>
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.<BR>
<BR>
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!!:<BR>
<BR>
Opening library file /gpfs/projects/ub51/ub51077/GROMACS-4.0-DEV/share/gromacs/top/aminoacids.dat<BR>There are: 157455 OTHER residues<BR>There are: 821 PROTEIN residues<BR>There are: 0 DNA residues<BR>
<BR>
The problem is that the program considers residues HIE out of the protein (histidines):<BR>
<BR>
0 System : 716705 atoms<BR> 1 Protein : 12658 atoms<BR> 2 Protein-H : 6344 atoms<BR> 3 C-alpha : 821 atoms<BR> 4 Backbone : 2463 atoms<BR> 5 MainChain : 3286 atoms<BR> 6 MainChain+Cb : 4038 atoms<BR> 7 MainChain+H : 4072 atoms<BR> 8 SideChain : 8586 atoms<BR> 9 SideChain-H : 3058 atoms<BR> 10 Prot-Masses : 12658 atoms<BR> 11 Non-Protein : 704047 atoms<BR> 12 HIE : 272 atoms<BR> 13 dop : 238464 atoms<BR> 14 SOL : 464400 atoms<BR> 15 Na : 467 atoms<BR> 16 Cl : 444 atoms<BR> 17 Other : 704047 atoms<BR><BR>
<BR>
I have tried to use both chains together and repeating the same, but the result is the same.<BR>
<BR>
What could I do? Anybody knows why there is a problem with HIE?<BR>
<BR>
Thank you very much in advance,<BR>
<BR>
Rebeca Garcia Fandiño<BR>
Parc Cientific de Barcelona<BR>
<BR>
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