AMBER Archive (2008)

Subject: Re: AMBER: solvateOct produces strange residues compared to solvateCap

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 10 2008 - 14:29:52 CDT

On Fri, Apr 04, 2008, Markus Kaukonen wrote:
>
> When solvating this molecule using tleap and solvateCap (AMBER9)
> everything is fine but when using instead
> solvateOct or sovateBox or solvateDontClip the first (H5O2) residue is
> split into pieces.

Try rearranging the order of atoms in the H5O2 residue, so that the first
three atoms are not O1, H11, H12. Of course, this is still a bug, some
someplace in the solvate code, LEaP is trying to recognize water molecules,
and is being too clever.

Might also be worth trying sleap (in AmberTools).

...good luck...dac

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