AMBER Archive (2009)

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

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Tue Jul 28 2009 - 05:28:40 CDT

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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