On Fri, Apr 02, 2010, Jio M wrote:
>
> I had same problem before also, subject being: "COOH group troubling"
>
> Now I have different molecule, whose N is to be further attached to
> other residues and then minimisation. But the COOH is showing undesired
> bond while doing minimisation. The RESP charges were derived. The bond
> is between C of carbonyl and H of OH. So a sort of triangle being
> formed.
Take a look at the ASH and GLH residues in the Amber libraries (and their
corresponding force field parameters.) These are neutral carboxylic acids,
and have been used a lot in real simulations, without the problems you
mention. See if there are differences between those parameters and yours.
...good luck....dac
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Received on Sat Apr 03 2010 - 08:00:03 PDT
