[gmx-users] multiple peptide simulation

[Mijiddorj B]

Dear All,
> If I have multiple peptides in my system and want to calculate
> inter-peptide hydrogen bonds, should I group all the peptides separately
> and calculate hydrogen bonds between every pair of peptide and sum them up?
>

The selection "Protein" can give you overall hydrogen bonds, however, if
you separately index the groups in those peptides, you can get more precise
numbers. There are some good options in gromacs to index groups. I
recommend you to calculate, separately, using some simple scripts such us
csh script with a loop.


> Or calculate overall no. of hydrogen bonds choosing the generic 'Protein'
> option from index file and divide by no. of peptides?
>
> If there are higher number of peptides, I guess that the results could be
closer. You can check.


> If its the former option, once we obtain a average no of h-bonds between
> two peptides, should we divide by half?
>
>
> Another question along similar lines is that if we carry out dssp analysis
> and we want to find out overall percentage of various secondary structures
> in the peptides, what option should we select in the index file? The
> generic 'Protein' option chooses all the peptides together. So if we choose
> that, the last line of scout.xvg (obtained from dssp) would show some
> percentage values. Is it for the overall system as I wanted?
>
> If I remember correctly, we usually chose the Mainchain option in the
index. If you can index separately, do_dssp can give you separate
percentages. Otherwise, the count is the overall value.
Finally, I recommend you work on indexing groups.

Please advise.
>
>
> Yours sincerely,
> Apramita
>
>
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