AMBER Archive (2005)

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

From: haixiao jin (jinhx952_at_gmail.com)
Date: Thu Oct 20 2005 - 21:03:43 CDT


thank you for your help! i had just solved my problem. the [:342_at_O] can be
recogized in distance command. the error message showed because i took a
mistaken. after Cl- added to neutralize the system, the number of water
molecule should be 346 instead of 342.
 the distance command, "distance 1 :346_at_O :173_at_OD1 out 1.list" was performed
OK.

 On 10/21/05, Thomas Cheatham <cheatham_at_chpc.utah.edu> wrote:
>
>
> > 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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