AMBER Archive (2009)

Subject: Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)

From: albert albert (albertassonke_at_googlemail.com)
Date: Fri Jul 31 2009 - 14:27:02 CDT

Thanks for all.

your explanation was very helpful .

Warm regard.

Albert

On Tue, Jul 28, 2009 at 12:28 PM, Ashish Runthala <ashish.runthala_at_gmail.com
> wrote:

> you can do with these grep commands, but it will do for all, and not
> all protons are insignificant. Remember here, that such protons seems
> weak bonds, but even then they are responsible for the stability of
> the overall confirmation. Check the structure in leap and protonate in
> a standard fashion, there, after removing the errors and warnings in
> leap.
> My advise is to properly verify the structure before stepping further.
> What you are working it out for by the way?
>
> Ashish
>
> On Mon, Jul 27, 2009 at 9:17 AM, Bill Ross<ross_at_cgl.ucsf.edu> wrote:
> >> how can I proceed to remove proton in protein
> >
> > % egrep -v H my.pdb > my_no_h.pdb
> >
> > Bill
> >
> > _______________________________________________
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> >
>
>
>
> --
> Ashish Runthala,
> Faculty Division III,
> Lecturer, Biological Sciences,
> Birla Institute of Technology and Science,
> Pilani, Rajasthan- 333031
> INDIA
>
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>
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