AMBER: ptraj hbond mask

From: Lars Skjærven <>
Date: Mon, 5 Nov 2007 17:00:03 +0100

Dear Amber user,

I am trying to calculate the hydrogen bonds between two monomers in a
complex. Due to the fact that hbond calculations are rather computationally
expensive (in terms of memory) I can only do this in the interface between
the two monomers. Hence, I need masks that specifies these areas in the two
monomers. I have used the ptraj script for calculating hbonds found here: However,
this will calculate all the hbonds in the complex and is by far too memory
expensive for my complex.

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.NZ :LYS.HZ1
acceptor mask :1-134,410-524.LYS.NZ :1-134,410-524.LYS.HZ1

to define the acceptors to be only in this area. Then the donors are defined
to be in:
donor mask :2000-2400,3150-3270.GLN.OE1

I would do this for every potential donor/acceptor atoms. This method yields
alot of warnings like:
"WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the"
so I suspect my masks are not that clever after all.. :-)

I tried to use the same masks in "ambmask" to check the masks, but I realise
the syntax used in ptraj and ambmask are not the same? I also checked to
find more documentation on this, but without any luck..

Thanks for any help :-)

Best regards,
Lars Skjaerven

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Received on Wed Nov 07 2007 - 06:07:25 PST
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