AMBER Archive (2007)

Subject: Re: AMBER: ptraj hbond mask

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Wed Nov 07 2007 - 15:00:40 CST

> I am trying to calculate the hydrogen bonds between two monomers in a
> complex. Due to the fact that hbond calculations are rather computationally
...
> So my question is: How can I write masks for finding hbonds between two
> monomers ? Or actually, between parts of two monomers..
>
> My suggestion was first to change
> acceptor mask :LYS_at_NZ :LYS_at_HZ1
> to
> acceptor mask :1-134,410-524_at_LYS@NZ :1-134,410-524_at_LYS@HZ1

Ah, your problem is the "@LYS" specification in the middle; you do not
want this. Without this, it should work, and if it doesn't either the
parsing routine is messing up or you have other residues in that range
that have NZ or HZ1 atoms (but not the other).

To avoid the potential for "messing up", try breaking up the
specification:

acceptor mask :1-134_at_NZ :1-134_at_HZ1
acceptor mask :410-524_at_NZ :410-524_at_HZ1

(no @LYS: @ is atom name)

Finally, if you still blow memory, what I tend to try is to create inputs
with fewer donors (or acceptors) and run the analysis twice (i.e. first
time with :1-134 and second time with :410-524).

-- tec3
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