Dear Ross,
Thanx for the reply. But I am still confused. I want to
know that if we don't cap the ends will it hamper the MD simulation. If I
want to do caping then what is the procedure. Please let me know.
On Mon, Apr 6, 2009 at 10:30 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Nicholus,
>
> If you want standard N and C terminal end groups then you do not need to do
> anything. Leap should take care of this. However, if you want different
> things such as neutral end groups or ACE / NME caps then you will need to
> modify the pdb.
>
> All the best
> Ross
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf
> Of nicholus bhattacharjee
> Sent: Monday, April 06, 2009 9:45 AM
> To: AMBER Mailing List
> Subject: [AMBER] Do I need to modify the cap residues
>
> Dear community,
> I wanted to know that do I need to modify the
> first and the last residues in a given PDB file to make it caped? Non of
> the
> tutorials have told about this thing. They only say about modifyins CYS,
> HIS
> residues. Please inform me about this and if I have to then what is the
> procedure.
>
> Thanking you,
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
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>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Wed Apr 08 2009 - 01:10:43 PDT
