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 - 08:08:48 CDT
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<fyd_at_q4md-forcefieldtools.org> 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
>> 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<ross_at_cgl.ucsf.edu> wrote:
>>>> how can I proceed to remove proton in protein
>>> % egrep -v H my.pdb > my_no_h.pdb
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