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 - 11:30:03 PDT
