AMBER Archive (2006)

Subject: Re[2]: AMBER: Could not find atom type.

From: Sergey Krishtal (skrishtal_at_mail.ru)
Date: Tue Apr 18 2006 - 21:56:30 CDT

The reason that I want to simulate ethanol as rigid molecule with two united atoms is that I need to simulate protein with ff03 force field and ethanol with OPLS UA force field. Therefore I know all potential parameters for ethanol and I don't need to use the antechamber program. As to ff03ua force field, I don't need methyl hydrogens of amino acid sidechains to be united to carbons.

Sergey

-----Original Message-----
From: "David A. Case" <case_at_scripps.edu>
To: amber_at_scripps.edu
Date: Tue, 18 Apr 2006 16:06:21 -0700
Subject: Re: AMBER: Could not find atom type.

>
> On Tue, Apr 18, 2006, Sergey Krishtal wrote:
>
> >
> > Ethanol molecule is supposed to be a rigid one with
> > two united atoms: CH3 and CH2.
>
> The straightforward approach in Amber is to treat ethanol as two carbons, one
> oxygen and 6 hydrogen atoms. The antechamber program can be used to create a
> forcefield for this that is consistent with the rest of the Amber force
> fields.
>
> It is not clear why you think that ethanol is "supposed" to have two united
> atoms, as above. This description might be consistent with ff03ua, but you
> should be sure that you have the background and experience to start creating
> a new forcefield when existing ones are already available.
>
> ....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