Re: [AMBER] water mediated H-Bond analysis

From: Daniel Roe <>
Date: Fri, 25 Feb 2011 07:25:56 -0500

Hi, my comments are below:

On Fri, Feb 25, 2011 at 3:32 AM, Sangita Kachhap <> wrote:
> When I increased value of solventneighbor from 5 to 12 it didnt give any warning
> According to manual solventneighbor specify maximum number of possible
> interactions per a given donor or acceptor.
> But I didnt get it so anyone please clear me this.

This is just a memory issue. The hbond command tends to use a large
amount of memory since it keeps a history of every hydrogen bond it
finds (which can be quite large when you include potential
interactions with solvent) so it is capped at 5.

> Mask [:1-24,26-43,45-47,48-57,59-73,75-146,.N] represents 142 atoms
> Mask [:1-211.H] represents 204 atoms
> WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
> atom selection in the two masks :1-24,26-43,45-47,48-57,59-73,75-146,.N and
> :1-211.H which contain 142 and 204
> atoms respectively.  Ignoring...
> Will it affect the final output of H-Bond analysis?

Yes, because right now your 'acceptor' command is being ignored. The
acceptor command assumes that each atom in the first mask (the 'heavy'
atom) is bonded to each atom in the second mask (the hydrogen atom);
this information is used to calculate angle. Why not specify "acceptor
mask :1-24,26-43,45-47,48-57,59-73,75-146.N
:1-24,26-43,45-47,48-57,59-73,75-146.H" or "acceptor mask :1-211.N


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Received on Fri Feb 25 2011 - 04:30:03 PST
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