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<ross.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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Received on Tue Jul 28 2009 - 10:08:44 PDT
