thank you for your help! i had just solved my problem. the [:342.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.O :173.OD1 out 1.list" was performed
OK.
On 10/21/05, Thomas Cheatham <cheatham.chpc.utah.edu> wrote:
>
>
> > Mask [:342.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.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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Received on Fri Oct 21 2005 - 03:53:00 PDT
