Re: [AMBER] water mediated H-Bond analysis

From: Sangita Kachhap <>
Date: Sat, 26 Feb 2011 15:49:14 +0530 (IST)

Thanks for reply

> 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
> :1-211.H"?

I have used these atom mask specification but again getting same warning

PTRAJ: acceptor mask :20-280.N :20-280.H
Mask [:20-280.N] represents 261 atoms
Mask [:20-280.H] represents 253 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :20-280.N and :20-280.H which contain 261 and 253
atoms respectively. Ignoring...

> -Dan
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Sangita Kachhap

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Received on Sat Feb 26 2011 - 02:30:03 PST
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