AMBER Archive (2009)

Subject: Re: [AMBER] RE: Listing gaff parameters in frcmod

From: Bokun Cho (chobokun9_at_yahoo.com)
Date: Fri May 08 2009 - 00:00:47 CDT

Thank you for your prompt reply, Asst. Prof Walker.
I am currently using AMBER 9 to simulate explicit solvation of organic molecules in organic solvents.
From tutorial 6, http://ambermd.org/tutorials/advanced/tutorial6/
The proton already has no VDW interactions hence removal of the charge will make it into a dummy atom. However this approach is not appropriate for my case as I have to make the whole organic molecule "disappear".

________________________________
From: Ross Walker <ross_at_rosswalker.co.uk>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Friday, 8 May 2009 12:34:08
Subject: RE: [AMBER] RE: Listing gaff parameters in frcmod

Hi Bokun,

You are probably better using the following tutorials:

http://ambermd.org/tutorials/advanced/tutorial6/

and

http://ambermd.org/tutorials/advanced/tutorial9/

In the case of AMBER 10 thermodynamic integration with soft core you no longer need to create dummy atoms.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Bokun Cho
> Sent: Thursday, May 07, 2009 9:21 PM
> To: amber_at_ambermd.org
> Subject: [AMBER] RE: Listing gaff parameters in frcmod
>
> I am trying to create a frcmod file to generate dummy atom parameters
> via the procedures in this tutorial http://ambermd.org/tutorial/shirts/
> Is there a command to list all the gaff parameters in the frcmod file
> or is there a simpler alternative method to generate dummy atoms? My
> molecule is larger and more complex than toluene.
> Thanks in advance for your help.
>
>
>
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