20 dec 2006 kl. 17.34 skrev OZGE ENGIN:
Hi,
I have some questions about g_hbond option.
1) My system consists of a protein molecule (a capped 1 alanine
residue) (CH3-CO-ALA-NH-CH3) and 250 water molecules. After
selecting the g_hbond option, it says that protein molecule
consists of 12 elements; however, it consists much more elements as
it can be seen. Could you explain the reason behind it?
It depends. Are you using a united atoms force field? If not, have
you had a look on which atoms are really part of the group "protein"?
It might be the case that the caps are not recognized as Protein. You
should probably make an index file with a index group specifying
exactly which atoms are part of your molecule and use the -n option
in g_hbond.
2) In order to investigate the Hydrogen bonds formed between water
molecules and the protein, should I select the protein and solvent
option? I selected like this, but I encountered with the following
error:
Range checking error:
Variable gx has value -3. It should have been within [ 0 .. 5 ]
Please report this to the mailing list ([email protected])
Hm. Don't know right away. Have to get back to you on that one.
3) In the output file of hbnum.xvg, there are three columns.I
think, the first column represents the time step, the second column
the number of hydrogen bonds. What about the third column?
That would be interactions fulfilling the distance criterion for h-
bonds (default is within 3.5 Å) but not the HDA angle criterion. This
can be seen in the header of the xvg-file (if one knows the file
format), or in the legend if one views the file in e.g. (xm)grace.
Thanks in advance
Özge ENGİN
Department of Computational Science and Engineering
Koc University, Istanbul
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