AMBER Archive (2009)

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

From: Ashish Runthala (
Date: Tue Jul 28 2009 - 08:08:48 CDT

Hello Fyd,
I know that to mention the options of hydrogens which needs to be
removed from the protein, you need to know the structure properly, So
either first make a list of all these hydrogens somewhere, and then
remove them by egrep or you can directly do it manually.
Anyways, but still i will say to watch out properly the confirmation
for the proper sampling.


On Tue, Jul 28, 2009 at 5:29 PM, FyD<> wrote:
> Dear Ashish Runthala,
>> 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?
> As said Bill egrep is perfect for that.
> You could egrep using specific hydrogen names.
> egrep -v "HB2|HB3" my.pdb > my_no-HB2HB3.pdb
> egrep -v "HA2|HA3|HB1|HB2|HB3" my.pdb > my_no-selected-H.pdb
> regards, Francois
>> On Mon, Jul 27, 2009 at 9:17 AM, Bill Ross<> 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

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