AMBER Archive (2006)

Subject: Re: AMBER: How to keep an hydrogen bond during an implicit MD calculation?

From: j j (fantvamp_at_gmail.com)
Date: Fri Dec 01 2006 - 04:59:59 CST

Maybe you can set nmropt=1 and the aply some dist restraints, in Amber 8
manual,
SANDER Input section FOUR Page 119
5.9. SECTION FOUR: Distance, angle and torsional restraints
JJ

2006/12/1, a a <patd_2_at_hotmail.com>:
>
> Dear Sir/Madam,
>
> Could you mind to let me know if I could fix some of the hydrogen bond
> form
> during a implicit solvent MD calculation?
>
> I tried to fix the involved atoms as group and references to the inpcrd
> file. However, the relative positions for the atoms are also fixed, while
> I
> could like to only keep those hydrogen bonds unbreak but relax the
> structures so that their relative positions could changes.
>
> If yes, how can I do it? Please kindly advice.
>
> Best regards,
> Annie
>
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