AMBER Archive (2009)

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

From: Bokun Cho (
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,
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 <>
To: AMBER Mailing List <>
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:


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

Good luck,

> -----Original Message-----
> From: [] On
> Behalf Of Bokun Cho
> Sent: Thursday, May 07, 2009 9:21 PM
> To:
> 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
> 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.
> Get your preferred Email name!
> Now you can and
> _______________________________________________
> AMBER mailing list

AMBER mailing list

      New Email names for you!
Get the Email name you&#39;ve always wanted on the new @ymail and @rocketmail.
Hurry before someone else does!
AMBER mailing list