AMBER Archive (2009)

Subject: Re: [AMBER] Do I need to modify the cap residues

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Mon Apr 06 2009 - 12:19:41 CDT

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_at_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_at_ambermd.org [mailto:amber-bounces_at_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)
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber