Re: [AMBER] 3NKB5

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 27 May 2014 06:20:14 -0400

On Tue, May 27, 2014 at 3:08 AM, ηŽ‹η <wangzhenzk.126.com> wrote:

> Hi Sir,
>
> Recently I use the Ambertools12 to protonate the N3 of the base Cytosine62
> of the nucleic, I find the model of pdb at the
> AmberTools12/amber12/dat/leap/prep/protonated_nucleic/RC+.pdb. but I do not
> realize how can I call the model to add the hydrogen according the RC+.pdb.
>
> I will deeply appreciate if you would like to tell me the solution.
>

​The protonated nucleic acids can be loaded into your leap session using
the command "loadOFF all_prot_nucleic10.lib". At that point, if you rename
the C 62 residue "CP" in your nucleic acid PDB file, leap will add
hydrogens according to the protonated Cytosine template.

HTH,
Jason
​ 
-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 27 2014 - 03:30:02 PDT
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