AMBER Archive (2007)

Subject: Re: AMBER: Problem with Antechamber and point charges

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Aug 01 2007 - 14:52:53 CDT

antechamber is for generating partial charges when none are
available. if you are just using standard protein residues, your
prmtop (built from leap) already has all of the partial charges in it.
you can use ambpdb (in amber) with the -pqr option to write a pdb
file that has the charges. grasp may or may not be able to read this-
if not, you might need to write a script to extract the charges and
convert to the proper format (I don't know what that is so I can't help).

On 8/1/07, anna duraj <annaduraj_at_gmail.com> wrote:
> Hi all!
>
> I am new user of AMBER and I have problem with getting atomic point charges
> for protein.
> My protein has approximately 300 residues. I want to create an input file
> for GRASP which has the charge info in it.
> I thought that Antechamber is the best for this, but when I use it , it
> gives me several errors.
> Can I use Antechamber for getting point charges in protein ? Or is it only
> for small molecules as eg.ligands??
> I am wondering If I can create such an input file using AMBER 9?
>
> Thanks in advance
>
> Anna
> 

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