AMBER Archive (2006)

Subject: Re: AMBER: GBSA implicit chloroform

From: nadiav_at_soton.ac.uk
Date: Wed Nov 01 2006 - 11:13:22 CST

Thank you for your help. That clarifies why I couldn't find any
information.

Nadia Vahdati

Quoting "David A. Case" <case_at_scripps.edu>:

> On Wed, Nov 01, 2006, nadiav_at_soton.ac.uk wrote:
> >
> > Is it possbile to use Chloroform or other solvents in GBSA apart from
> water
> > and how?
>
> Basically, implicit solvation in Amber is only for water. You could try
> to use
> a lower value of extdiel, but that probably doesn't capture the real
> behavior
> of chloroform. Among other things, the GB radii are optimized for water
> simulations, not for any other solvent.
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu