Thank you very much for the information!
Song-Ho
2016-09-19 3:04 GMT+09:00 Jason Swails <jason.swails.gmail.com>:
> On Sun, Sep 18, 2016 at 12:21 PM, Song-Ho Chong <chong.sookmyung.ac.kr>
> wrote:
> >
> > (1) yields the amber topology in which the water residue name is TIP3
> > and water atom names are OH2, H1, H2 (charmm convention),
> >
> > whereas
> >
> > (2) yields the amber topology in which the water residue and atom
> > names are converted to WAT, O, H1, H2 (amber convention).
> >
>
> This is the main difference causing the problem.
>
> The solution is simple -- use the WATNAM and OWTNM variables in the &cntrl
> namelist to set water recognition to find waters named TIP3 and oxygen
> atoms named OH2, respectively.
>
> This has been discussed a few times in the past on the list. For example,
> here: http://archive.ambermd.org/201410/0452.html
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Sun Sep 18 2016 - 18:00:02 PDT
