Re: AMBER: Problem with Antechamber and point charges

From: anna duraj <>
Date: Fri, 3 Aug 2007 15:47:17 -0400


Thanks Carlos. It was really helpful.
I have one more problem. I need to create charge file to GRASP (amber.crg),
but I need in it also radius. I tried to set up xleap and extract them to
file. I tried also ambpdb but it didn't work.
Does somoneone know how create Radius/Charge file which will be read by

Thanks in advance


On 8/1/07, Carlos Simmerling <> wrote:
> 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 <> 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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Received on Sun Aug 05 2007 - 06:07:57 PDT
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