AMBER Archive (2009)

Subject: Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Wed Jun 10 2009 - 20:02:51 CDT

I think you need to run your vdW-only alchemical mutation step
independently of the charge-removal step. Not sure what you mean by
"last" quadrature point, as these can be independent of each other as
well (and, indeed, are in Thomas' tutorial). Minimize, heat, and
equilibrate with v0=TYR and v1=PHE. Then you will end up with
coordinates for PHE to use in your production run.

--Tom

On Wed, Jun 10, 2009 at 4:27 PM, Jodi Hadden<jodih_at_uga.edu> wrote:
> The error tells me that for my v1 process, my topology and coordinate
> files don’t match in atom number. I understand this, since the
> topology file is for PHE while the input coordinate file is from the
> data collection MD of the last point of quadrature from step one,
> where the partial charges of TYR were being removed, and therefore
> refers to atoms for TYR, not PHE. What I do not understand is:  if I
> can’t use this for my input coordinate file for the v1 process, what
> am I supposed to use?

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