AMBER Archive (2005)

Subject: Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Thu Oct 20 2005 - 20:50:43 CDT

> Mask [:342_at_O] represents O atoms!!!!! NO ATOMS DETECTED!!!

If ptraj does not find this, either there is an error with the program or
residue 342 atom named O does not exist.

Using rdparm, you can

   checkmask :342_at_O

or

   atoms :342

and see if residue 342 has an atom named O in it; perhaps the name is
different than you think or you have the incorrect residue number?

Note that the notion of crystal waters is tricky in MD simulation since
water is highly mobile and therefore they exchange rapidly. Even at tight
interfaces, such as a protein-nucleic acid interface, the lifetimes of
bound water are on the ns time scale.

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