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.
Ashish
On Tue, Jul 28, 2009 at 5:29 PM, FyD<fyd.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
>> 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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--
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA
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Received on Tue Jul 28 2009 - 10:09:16 PDT
