AMBER Archive (2008)

Subject: Re: AMBER: Hydroxyprolines!!!

From: David A. Case (case_at_scripps.edu)
Date: Wed May 07 2008 - 20:26:16 CDT

On Wed, May 07, 2008, Titus, Jamie (bairdje) wrote:
>
> The hydroxyproline forcefield parameters use
> the atom type 'OO' which I do not see in the mdread.f file. Will I need to
> add this atom type to this file to be able to calculate surface areas of
> molecules containing hydroxyproline?

Yes...but presumably, you want the LCPO parameters for the OH group in
hydroxyproline to be the same as the ones of the OH group in serine or
threonine. So, modify mdread.f in the way you suggest, but make sure the the
parameters you are copying into the "OO" section match those for a ser/thr
OH group.

...good luck...dac

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