AMBER Archive (2008)

Subject: Re: AMBER: About antechamber and GAFF [UPDATED]

From: Navnit Kumar Mishra (navnit_at_chemi.muni.cz)
Date: Wed Nov 26 2008 - 07:04:20 CST

Hello Abel;

redefined the atom types in capital letter of your prep file. As you
know the GAFF define the atom types in small letters.

navnit

Stephane Abel wrote:
> My last message was not very clear,
>
>
> Below the correct message
>
>
> Hi AMBER users
>
>
> I have two little questions about GAFF and Antechamber. Last week I
> asked a question about simulations with glycolipid with AMBER force
> field (Glycam06 in this case). I received a response of David A Case
> and Mattew Tessier. They said me that a good starting point for using
> AMBER force field and obtain the partial charge of the molecule is to
> use Antechamber. So I have installed Ambertools without any problems
> and started the tutorials, especially the example B4 of Ross Walker.
> If understand well, Antechamber use Gaff for the assignation of the
> parameters of the molecule. I try with GAFF, and indeed i obtained the
> partial charges, for my molecule. Here come my questions, it is
> possible to change this force field and use Glycam06 ? Because I want
> to use only Glycam for my MD If yes, how I can do it ?
>
>
> Thank in advance for your help
>
>
> stefane
>
> -----------------------------------------------------------------------
> 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
>
>
> -----------------------------------------------------------------------
> 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
>

-----------------------------------------------------------------------
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