ptraj can dump the radii using the dumpq command.
be careful with what you mean by "radii", is it the vdw radii,
radii for solvation, etc.
On 8/3/07, anna duraj <annaduraj.gmail.com> wrote:
> Hi
>
> 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
> GRASP?
>
> Thanks in advance
>
> Anna
>
>
> On 8/1/07, Carlos Simmerling <carlos.simmerling.gmail.com> 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 <annaduraj.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
> > >
> >
> >
> > --
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 05 2007 - 06:07:57 PDT
