AMBER Archive (2002)

Subject: Re: NMR refinement

From: A. Hungie (hungie01_at_hotmail.com)
Date: Thu May 16 2002 - 10:02:17 CDT

>We have a paper in press in J. Biomol. NMR about using GB and explicit
>water
>for refinements of proteins, and another paper (still in preparation) about
>results with DNA. Briefly, either GB or explicit water is better than
>vacuum refinements. For most purposes, GB is faster and easier to use, and
>is what we recommend.
>

Dear David Case and Other amber's users,

I am not clear in some points.

1. For GB (implicit water) calculation,
   - did you neutralize DNA system with Na+ ions?
   - did you apply PME method for GB?

2. If the system is not neutralized,
   - is there any problem with periodic boundary condition, e.g. summation
of charge? As my understanding, total charge may be infinity.
   - how amber treat the non-neutral system for applying PME?

Thank you very much for any suggestion in advance.

Regards,
Hungie

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