AMBER Archive (2009)
Subject: Re: [AMBER] COOH group troubling
From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sun Dec 06 2009 - 10:46:58 CST
> I have a docked ligand which has COOH group.=20
> When I do minimisation, there are stars ****** in mdout.
> I obtained rst file from small steps minimisation ...
> and got the pdb. I found that O oxygen of C=3DO and O oxygen of C-OH
> bond with each other.
The pdb does not contain bonding info, so the bonds shown in the
viewer are often 'best guess' based on known residue bonding patterns
and/or distances, depending on the pdb view program. So the bond you
are seeing is likely not an actual bond, just a short distance.
It's odd that 2 O's are getting close, since they are likely both
To be sure the COOH group is the problem, in your minimization .out
file, see which atom is reported for gradient max (GMAX).
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