[AMBER] water mediated H-Bond analysis

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Fri, 25 Feb 2011 14:02:10 +0530 (IST)

Hi All

I am doing water mediated H-bond analysis for Protein-DNA complex so I use the
following command:

hbond solventneighbor 5 solventdonor WAT O solventacceptor WAT O H1
solventacceptor WAT O H2 time 2 print .05 series hbt

and it gave following warning :

WARNING in ptraj(), hbond: Too many solvent acceptors near donor atom 374
(:13.O2P )! (set solventneighor higher)

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.

One more thing when using
acceptor mask :1-24,26-43,45-47,48-57,59-73,75-146,.N :1-211.H

It giving output like this:

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?

Sangita Kachhap

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Received on Fri Feb 25 2011 - 01:00:03 PST
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