Hi Chris and amber users,
Thank you very much for your email. I am trying to create a pdb file in
pdbq format using amber.
While calculating the charge I want to use all hydrogen but later i want to
remove non-polar hydrogens
by adding their charge onto the carbon atom(to get a pdb file with nonpolar
hydrogen only).
thanks
s
On 8/27/07, Chris Moth <chris.moth.vanderbilt.edu> wrote:
>
> I don't understand exactly what you are parameterizing - but you may find
> this paper helpful:
>
> J. Phys. Chem. B, 110 (26), 13166 -13176, 2006. 10.1021/jp060163v
> S1520-6106(06)00163-5
> Web Release Date: June 15, 2006
>
> Copyright (c) 2006 American Chemical Society
> New-Generation Amber United-Atom Force Field
>
> Lijiang Yang, Chun-hu Tan, Meng-Juei Hsieh, Junmei Wang, Yong Duan, Piotr
> Cieplak, James Caldwell, Peter A. Kollman,# and Ray Luo*
>
> This united-atom forcefield is available in Amber 9. So, you can look in
> the parameter files to see how residue data is assembled.
>
> You might contact the authors to see if any automated scripts are
> available to collapse the hydrogen charges onto the carbons.
>
> One caveat: This forcefield currently lacks parameterization for
> cross-linked cysteines.
>
>
>
>
>
>
>
>
> > Dear Users,
> > I am trying to add hydrogen in PDB file inside amber and then
> calculating
> > the charges.
> > But in next step i want to remove non-polar hydrogens by adding their
> > charge
> > onto the
> > carbon atom. Is it possible to do such calculation inside amber? thank
> you
> > in advance
> > for your timely help.
> > s
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Aug 29 2007 - 06:07:32 PDT
