AMBER Archive (2008)

Subject: Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop

From: Grange Hermitage (ghermitage_at_gmail.com)
Date: Mon Jul 14 2008 - 02:41:40 CDT

Thanks, Ross.

The CHU and CHV are covalently connected.
I tried defining this using gromacs rtp entries in ffG43a2 and OPLS, both
based on serine and taking all defaults, but the systems produced are
unstable.

The advice being reinforced by my experiences there is that when extending a
force field you must go back to methods originally used to define the force
field. I am using GAFF because it is a complete force field.

On Mon, Jul 14, 2008 at 2:05 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

>
> In fact in your case your system comprises a number of individual residues
> so you probably shouldn't be using antechamber at all and it is not clear to
> me why you want to do it this way. Except for the CHU, AIB and CHV
> everything looks to be standard residues
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu