AMBER Archive (2004)

Subject: Re: AMBER: Problem with a single aminoacid as inhibitor

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Nov 17 2004 - 06:43:08 CST

I'm not positive that I understand, but maybe using a different name for
it would
work (if it is a SER, call it NSER). This will indicate to leap that it
should use the
N-terminal form.
Carlos

Daniel Wetzler wrote:

> Dear Amber-users,
>
> I have a problem with a single aminoacid which acts like a inhibitor for
> a enzyme I'm dealing with.
> My problem is, that this aminoacid should be fully protonated
> (NH3-group).
> Regardless how I write this structure into my pdb-files (in its own
> chain, as HETATM
> a.s.o) xleap seems to handle it like a part of my structure and
> protonates my N only with one H.
>
> If I protonate my structure with the protonate command I get the right
> structure with NH3
> but after using xleap to write the .top / .crd files I get the
> deprotonated form again.
>
> Does anyone know how to change that behaviour ?
>
> Hope anyone can help.
>
> Best wishes,
>

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