From: Daniel Roe <>
Date: Mon, 13 Jan 2020 12:08:01 -0500


On Mon, Jan 13, 2020 at 10:49 AM Rui Chen <> wrote:

> 1. Should I specify the protein/ligand mask by using "hbond :1-432,433" and
> add "nointramol" at the end of the command?

If you don't care about intra-molecular hydrogen bonds (i.e. you want
the inter-molecular hydrogen bonds) then sure.

> 2. Residues 417 to 432 are glycans, do I need to include them in the
> calculation?

Only if you want to see if they hydrogen bond.

> 3. Is it correct to analyze all the solvent H-bond interactions (There are
> more than 30,000 water atoms in my system) or specify important waters
> (i.g. within 10 angstrom of protein and ligand)? What do researchers
> usually do?

Whether you want to look at solvent-solute hydrogen bonds really
varies depending on what you want to learn. If you want to ascertain
whether structured waters might be important (which can in turn be
inferred from long solute-solvent hydrogen bond lifetimes), or if you
suspect bridging waters may be important, then by all means look at
them. Be aware that this will result in a lot more bonds to look at,
and may take up a ton of memory if 'series' is also specified.

> 4. Then how to specify waters within 10 angstrom of protein and ligand?

It's unclear to me why you need this in the context of hydrogen bond
analysis (if a water is hydrogen bonding it must be within 10
angstroms). However, you can use distance-dependent atom masks, but
those do not update on a per-frame basis (the reasons are discussed in
the cpptraj manual) so your best bet is probably to use the
'watershell' command to determine how many waters are within 10
angstroms of the protein and ligand, then use the 'closest' command to
retain that many waters, then you'll have a consistent system on a
frame-by-frame basis (although again its unclear to me what you're
looking for here so this may not be useful to you).


> Looking forward to your reply.
> Best regards,
> Rui
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Received on Mon Jan 13 2020 - 09:30:01 PST
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